Starting phenix.real_space_refine on Tue Feb 13 10:18:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghb_40039/02_2024/8ghb_40039_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghb_40039/02_2024/8ghb_40039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghb_40039/02_2024/8ghb_40039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghb_40039/02_2024/8ghb_40039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghb_40039/02_2024/8ghb_40039_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghb_40039/02_2024/8ghb_40039_updated.pdb" } resolution = 2.76 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= 0.000 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: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 34 5.16 5 C 3379 2.51 5 N 920 2.21 5 O 955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5289 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5288 Classifications: {'peptide': 658} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 614} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.73, per 1000 atoms: 0.71 Number of scatterers: 5289 At special positions: 0 Unit cell: (75.44, 62.32, 107.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 34 16.00 O 955 8.00 N 920 7.00 C 3379 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: 2.96 Conformation dependent library (CDL) restraints added in 1.0 seconds 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 4 sheets defined 42.7% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 168 through 191 removed outlier: 3.519A pdb=" N TYR A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 225 through 234 removed outlier: 4.168A pdb=" N PHE A 232 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 337 through 356 Processing helix chain 'A' and resid 365 through 378 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 424 through 435 removed outlier: 3.621A pdb=" N ALA A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 459 through 482 Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 493 through 503 Processing helix chain 'A' and resid 522 through 544 removed outlier: 4.683A pdb=" N GLN A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N HIS A 540 " --> pdb=" O CYS A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 574 through 580 Processing helix chain 'A' and resid 584 through 596 Processing helix chain 'A' and resid 618 through 644 removed outlier: 4.219A pdb=" N GLN A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.500A pdb=" N GLU A 47 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 80 " --> pdb=" O ALA A 9 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 12 through 14 removed outlier: 3.666A pdb=" N ALA A 12 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 32 through 39 removed outlier: 3.808A pdb=" N LEU A 24 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 37 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 273 through 277 removed outlier: 3.569A pdb=" N VAL A 301 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 315 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LYS A 304 " --> pdb=" O PRO A 313 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 633 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: 1.51 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1689 1.34 - 1.46: 882 1.46 - 1.57: 2806 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 5428 Sorted by residual: bond pdb=" CG1 ILE A 357 " pdb=" CD1 ILE A 357 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.21e+00 bond pdb=" CB PRO A 555 " pdb=" CG PRO A 555 " ideal model delta sigma weight residual 1.492 1.425 0.067 5.00e-02 4.00e+02 1.81e+00 bond pdb=" C ILE A 390 " pdb=" N PRO A 391 " ideal model delta sigma weight residual 1.337 1.353 -0.016 1.24e-02 6.50e+03 1.66e+00 bond pdb=" CA ILE A 390 " pdb=" C ILE A 390 " ideal model delta sigma weight residual 1.524 1.538 -0.013 1.05e-02 9.07e+03 1.62e+00 bond pdb=" CG GLU A 267 " pdb=" CD GLU A 267 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.54e+00 ... (remaining 5423 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.64: 230 106.64 - 113.70: 2915 113.70 - 120.75: 2400 120.75 - 127.81: 1757 127.81 - 134.87: 76 Bond angle restraints: 7378 Sorted by residual: angle pdb=" N PRO A 443 " pdb=" CA PRO A 443 " pdb=" C PRO A 443 " ideal model delta sigma weight residual 110.70 115.33 -4.63 1.22e+00 6.72e-01 1.44e+01 angle pdb=" CA ILE A 390 " pdb=" C ILE A 390 " pdb=" N PRO A 391 " ideal model delta sigma weight residual 118.88 124.08 -5.20 1.54e+00 4.22e-01 1.14e+01 angle pdb=" CA PRO A 443 " pdb=" C PRO A 443 " pdb=" N PRO A 444 " ideal model delta sigma weight residual 117.93 121.92 -3.99 1.20e+00 6.94e-01 1.11e+01 angle pdb=" CA PRO A 391 " pdb=" N PRO A 391 " pdb=" CD PRO A 391 " ideal model delta sigma weight residual 112.00 107.64 4.36 1.40e+00 5.10e-01 9.70e+00 angle pdb=" CA THR A 327 " pdb=" CB THR A 327 " pdb=" CG2 THR A 327 " ideal model delta sigma weight residual 110.50 115.56 -5.06 1.70e+00 3.46e-01 8.86e+00 ... (remaining 7373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 2968 17.33 - 34.66: 236 34.66 - 51.99: 37 51.99 - 69.32: 16 69.32 - 86.65: 4 Dihedral angle restraints: 3261 sinusoidal: 1348 harmonic: 1913 Sorted by residual: dihedral pdb=" CA ASP A 335 " pdb=" C ASP A 335 " pdb=" N PRO A 336 " pdb=" CA PRO A 336 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA THR A 537 " pdb=" C THR A 537 " pdb=" N ALA A 538 " pdb=" CA ALA A 538 " ideal model delta harmonic sigma weight residual -180.00 -161.47 -18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LEU A 382 " pdb=" C LEU A 382 " pdb=" N HIS A 383 " pdb=" CA HIS A 383 " ideal model delta harmonic sigma weight residual -180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 3258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 669 0.067 - 0.133: 117 0.133 - 0.200: 7 0.200 - 0.266: 2 0.266 - 0.333: 1 Chirality restraints: 796 Sorted by residual: chirality pdb=" CB THR A 327 " pdb=" CA THR A 327 " pdb=" OG1 THR A 327 " pdb=" CG2 THR A 327 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB ILE A 390 " pdb=" CA ILE A 390 " pdb=" CG1 ILE A 390 " pdb=" CG2 ILE A 390 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU A 303 " pdb=" CB LEU A 303 " pdb=" CD1 LEU A 303 " pdb=" CD2 LEU A 303 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 793 not shown) Planarity restraints: 959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 185 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C MET A 185 " -0.051 2.00e-02 2.50e+03 pdb=" O MET A 185 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 186 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 335 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.31e+00 pdb=" N PRO A 336 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 80 " -0.227 9.50e-02 1.11e+02 1.02e-01 6.76e+00 pdb=" NE ARG A 80 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 80 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 80 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 80 " -0.005 2.00e-02 2.50e+03 ... (remaining 956 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 62 2.64 - 3.20: 4496 3.20 - 3.77: 9281 3.77 - 4.33: 12690 4.33 - 4.90: 20291 Nonbonded interactions: 46820 Sorted by model distance: nonbonded pdb=" OXT ILE A 663 " pdb="FE FE2 A 901 " model vdw 2.072 3.000 nonbonded pdb=" NE2 HIS A 360 " pdb="FE FE2 A 901 " model vdw 2.150 3.080 nonbonded pdb=" NE2 HIS A 365 " pdb="FE FE2 A 901 " model vdw 2.222 3.080 nonbonded pdb=" O SER A 594 " pdb=" OG SER A 598 " model vdw 2.289 2.440 nonbonded pdb=" O ILE A 371 " pdb=" OG1 THR A 375 " model vdw 2.302 2.440 ... (remaining 46815 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: 1.720 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: 0.010 Extract box with map and model: 7.100 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 20.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 0.067 5428 Z= 0.380 Angle : 0.821 9.866 7378 Z= 0.425 Chirality : 0.052 0.333 796 Planarity : 0.009 0.102 959 Dihedral : 13.616 86.652 2021 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.29), residues: 654 helix: -1.16 (0.25), residues: 291 sheet: 0.65 (0.56), residues: 78 loop : -0.55 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 208 HIS 0.014 0.002 HIS A 360 PHE 0.023 0.002 PHE A 94 TYR 0.013 0.002 TYR A 97 ARG 0.020 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.663 Fit side-chains REVERT: A 5 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8174 (tpt-90) REVERT: A 32 GLU cc_start: 0.8477 (pt0) cc_final: 0.8234 (pt0) REVERT: A 68 HIS cc_start: 0.7788 (t70) cc_final: 0.7329 (t70) REVERT: A 110 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 435 GLN cc_start: 0.8766 (tt0) cc_final: 0.8428 (mp10) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 1.3868 time to fit residues: 153.9663 Evaluate side-chains 58 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5428 Z= 0.222 Angle : 0.549 7.192 7378 Z= 0.277 Chirality : 0.040 0.153 796 Planarity : 0.005 0.048 959 Dihedral : 4.362 15.673 715 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.64 % Allowed : 10.72 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.31), residues: 654 helix: 0.29 (0.29), residues: 291 sheet: 0.49 (0.54), residues: 72 loop : -0.14 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 498 HIS 0.012 0.001 HIS A 51 PHE 0.010 0.001 PHE A 482 TYR 0.009 0.001 TYR A 474 ARG 0.006 0.000 ARG A 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.601 Fit side-chains REVERT: A 5 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8536 (ttm-80) REVERT: A 21 ARG cc_start: 0.7219 (tpt90) cc_final: 0.6993 (tpt170) REVERT: A 32 GLU cc_start: 0.8401 (pt0) cc_final: 0.7990 (pt0) REVERT: A 68 HIS cc_start: 0.7834 (t70) cc_final: 0.7609 (t-170) REVERT: A 82 THR cc_start: 0.9211 (p) cc_final: 0.8774 (t) REVERT: A 110 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 133 LYS cc_start: 0.8391 (mttt) cc_final: 0.8035 (mtpp) REVERT: A 159 ASP cc_start: 0.8498 (m-30) cc_final: 0.8178 (m-30) REVERT: A 168 GLU cc_start: 0.8151 (tp30) cc_final: 0.7915 (tp30) REVERT: A 435 GLN cc_start: 0.8785 (tt0) cc_final: 0.8413 (mp10) REVERT: A 574 MET cc_start: 0.8035 (tpp) cc_final: 0.7816 (tpp) REVERT: A 589 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8090 (tt) REVERT: A 651 TYR cc_start: 0.8795 (m-80) cc_final: 0.8487 (m-10) outliers start: 15 outliers final: 3 residues processed: 74 average time/residue: 1.3043 time to fit residues: 100.7120 Evaluate side-chains 64 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5428 Z= 0.214 Angle : 0.520 7.821 7378 Z= 0.257 Chirality : 0.040 0.148 796 Planarity : 0.004 0.046 959 Dihedral : 4.098 14.970 715 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.99 % Allowed : 12.65 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.32), residues: 654 helix: 1.06 (0.30), residues: 290 sheet: 0.51 (0.54), residues: 72 loop : 0.16 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 498 HIS 0.010 0.001 HIS A 51 PHE 0.011 0.001 PHE A 482 TYR 0.009 0.001 TYR A 474 ARG 0.006 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.484 Fit side-chains REVERT: A 32 GLU cc_start: 0.8373 (pt0) cc_final: 0.8027 (pt0) REVERT: A 68 HIS cc_start: 0.7850 (t70) cc_final: 0.7590 (t-170) REVERT: A 110 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7453 (tm-30) REVERT: A 133 LYS cc_start: 0.8360 (mttt) cc_final: 0.7927 (tppt) REVERT: A 156 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7512 (ptm-80) REVERT: A 159 ASP cc_start: 0.8523 (m-30) cc_final: 0.8125 (m-30) REVERT: A 164 MET cc_start: 0.7162 (ptp) cc_final: 0.6870 (ptm) REVERT: A 435 GLN cc_start: 0.8808 (tt0) cc_final: 0.8374 (mp10) REVERT: A 589 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8178 (tt) REVERT: A 603 ASP cc_start: 0.8678 (t0) cc_final: 0.8161 (t0) REVERT: A 651 TYR cc_start: 0.8762 (m-80) cc_final: 0.8431 (m-10) outliers start: 17 outliers final: 4 residues processed: 73 average time/residue: 1.2127 time to fit residues: 92.7125 Evaluate side-chains 64 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5428 Z= 0.265 Angle : 0.533 7.751 7378 Z= 0.262 Chirality : 0.040 0.147 796 Planarity : 0.004 0.045 959 Dihedral : 4.066 14.755 715 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.69 % Allowed : 13.36 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.32), residues: 654 helix: 1.32 (0.30), residues: 292 sheet: 0.40 (0.55), residues: 72 loop : 0.30 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 498 HIS 0.008 0.001 HIS A 51 PHE 0.012 0.001 PHE A 482 TYR 0.009 0.001 TYR A 460 ARG 0.005 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8373 (pt0) cc_final: 0.8022 (pt0) REVERT: A 55 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7743 (pt0) REVERT: A 110 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7593 (tm-30) REVERT: A 133 LYS cc_start: 0.8377 (mttt) cc_final: 0.7935 (tppt) REVERT: A 156 ARG cc_start: 0.7938 (ttp-110) cc_final: 0.7558 (ptm-80) REVERT: A 158 ASP cc_start: 0.8380 (m-30) cc_final: 0.8063 (m-30) REVERT: A 159 ASP cc_start: 0.8538 (m-30) cc_final: 0.8087 (m-30) REVERT: A 435 GLN cc_start: 0.8865 (tt0) cc_final: 0.8338 (mp10) REVERT: A 589 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8141 (tt) REVERT: A 603 ASP cc_start: 0.8725 (t0) cc_final: 0.8182 (t0) REVERT: A 651 TYR cc_start: 0.8787 (m-80) cc_final: 0.8497 (m-10) outliers start: 21 outliers final: 7 residues processed: 79 average time/residue: 1.3012 time to fit residues: 107.3235 Evaluate side-chains 69 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 0.0060 chunk 21 optimal weight: 3.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 101 GLN A 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5428 Z= 0.240 Angle : 0.535 7.384 7378 Z= 0.264 Chirality : 0.041 0.229 796 Planarity : 0.004 0.044 959 Dihedral : 4.016 14.407 715 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.69 % Allowed : 13.71 % Favored : 82.60 % 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: 1.17 (0.33), residues: 654 helix: 1.42 (0.30), residues: 293 sheet: 0.34 (0.56), residues: 72 loop : 0.37 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 498 HIS 0.007 0.001 HIS A 51 PHE 0.012 0.001 PHE A 278 TYR 0.009 0.001 TYR A 460 ARG 0.004 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8377 (pt0) cc_final: 0.8009 (pt0) REVERT: A 98 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8105 (ptp-110) REVERT: A 110 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 156 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7553 (ptm-80) REVERT: A 159 ASP cc_start: 0.8493 (m-30) cc_final: 0.8042 (m-30) REVERT: A 435 GLN cc_start: 0.8849 (tt0) cc_final: 0.8336 (mp10) REVERT: A 589 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8133 (tt) REVERT: A 603 ASP cc_start: 0.8745 (t0) cc_final: 0.8158 (t0) REVERT: A 651 TYR cc_start: 0.8786 (m-80) cc_final: 0.8492 (m-10) outliers start: 21 outliers final: 5 residues processed: 76 average time/residue: 1.3255 time to fit residues: 104.9699 Evaluate side-chains 64 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5428 Z= 0.194 Angle : 0.532 8.319 7378 Z= 0.261 Chirality : 0.040 0.209 796 Planarity : 0.004 0.044 959 Dihedral : 3.952 14.193 715 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.34 % Allowed : 14.94 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.33), residues: 654 helix: 1.52 (0.30), residues: 293 sheet: 0.26 (0.56), residues: 72 loop : 0.40 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 70 HIS 0.007 0.001 HIS A 51 PHE 0.010 0.001 PHE A 482 TYR 0.008 0.001 TYR A 474 ARG 0.007 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.657 Fit side-chains REVERT: A 32 GLU cc_start: 0.8416 (pt0) cc_final: 0.8030 (pt0) REVERT: A 40 ARG cc_start: 0.8015 (mmt90) cc_final: 0.7726 (mmt90) REVERT: A 156 ARG cc_start: 0.7924 (ttp-110) cc_final: 0.7558 (ptm-80) REVERT: A 159 ASP cc_start: 0.8482 (m-30) cc_final: 0.8033 (m-30) REVERT: A 168 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7814 (mm-30) REVERT: A 219 ARG cc_start: 0.8160 (tmt-80) cc_final: 0.7480 (tpt90) REVERT: A 435 GLN cc_start: 0.8875 (tt0) cc_final: 0.8350 (mp10) REVERT: A 548 LEU cc_start: 0.8961 (tp) cc_final: 0.8705 (tm) REVERT: A 589 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8059 (tt) REVERT: A 603 ASP cc_start: 0.8731 (t0) cc_final: 0.8136 (t0) REVERT: A 651 TYR cc_start: 0.8787 (m-80) cc_final: 0.8502 (m-10) outliers start: 19 outliers final: 5 residues processed: 77 average time/residue: 1.1787 time to fit residues: 95.0030 Evaluate side-chains 66 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5428 Z= 0.313 Angle : 0.580 7.979 7378 Z= 0.284 Chirality : 0.042 0.193 796 Planarity : 0.004 0.043 959 Dihedral : 4.012 14.798 715 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.99 % Allowed : 15.99 % Favored : 81.02 % 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: 1.27 (0.33), residues: 654 helix: 1.51 (0.30), residues: 294 sheet: 0.23 (0.55), residues: 72 loop : 0.44 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 176 HIS 0.006 0.001 HIS A 51 PHE 0.014 0.001 PHE A 278 TYR 0.010 0.001 TYR A 460 ARG 0.007 0.001 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.657 Fit side-chains REVERT: A 32 GLU cc_start: 0.8439 (pt0) cc_final: 0.8067 (pt0) REVERT: A 98 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8086 (ptp-110) REVERT: A 156 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7559 (ptm-80) REVERT: A 159 ASP cc_start: 0.8523 (m-30) cc_final: 0.8037 (m-30) REVERT: A 168 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7742 (tp30) REVERT: A 219 ARG cc_start: 0.8146 (tmt-80) cc_final: 0.7429 (tpt90) REVERT: A 435 GLN cc_start: 0.8838 (tt0) cc_final: 0.8311 (mp10) REVERT: A 485 ARG cc_start: 0.8485 (mtp85) cc_final: 0.7929 (mtp85) REVERT: A 548 LEU cc_start: 0.8943 (tp) cc_final: 0.8692 (tm) REVERT: A 589 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8128 (tt) REVERT: A 603 ASP cc_start: 0.8765 (t0) cc_final: 0.8176 (t0) REVERT: A 651 TYR cc_start: 0.8847 (m-80) cc_final: 0.8519 (m-10) outliers start: 17 outliers final: 5 residues processed: 74 average time/residue: 1.2259 time to fit residues: 94.9672 Evaluate side-chains 69 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5428 Z= 0.250 Angle : 0.570 8.009 7378 Z= 0.277 Chirality : 0.041 0.188 796 Planarity : 0.004 0.043 959 Dihedral : 3.997 14.851 715 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.16 % Allowed : 16.34 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.33), residues: 654 helix: 1.57 (0.30), residues: 293 sheet: 0.14 (0.55), residues: 74 loop : 0.45 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.006 0.001 HIS A 51 PHE 0.013 0.001 PHE A 278 TYR 0.009 0.001 TYR A 460 ARG 0.006 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.636 Fit side-chains REVERT: A 32 GLU cc_start: 0.8436 (pt0) cc_final: 0.8066 (pt0) REVERT: A 98 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8075 (ptp-110) REVERT: A 156 ARG cc_start: 0.7987 (ttp-110) cc_final: 0.7609 (ptm-80) REVERT: A 159 ASP cc_start: 0.8538 (m-30) cc_final: 0.8036 (m-30) REVERT: A 168 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7782 (tp30) REVERT: A 219 ARG cc_start: 0.8148 (tmt-80) cc_final: 0.7441 (tpt90) REVERT: A 263 GLN cc_start: 0.7523 (mt0) cc_final: 0.7162 (mt0) REVERT: A 435 GLN cc_start: 0.8851 (tt0) cc_final: 0.8319 (mp10) REVERT: A 548 LEU cc_start: 0.8931 (tp) cc_final: 0.8677 (tm) REVERT: A 589 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8140 (tt) REVERT: A 603 ASP cc_start: 0.8735 (t0) cc_final: 0.8122 (t0) REVERT: A 651 TYR cc_start: 0.8804 (m-80) cc_final: 0.8525 (m-10) outliers start: 18 outliers final: 7 residues processed: 78 average time/residue: 1.2772 time to fit residues: 103.9598 Evaluate side-chains 69 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 646 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5428 Z= 0.245 Angle : 0.572 7.875 7378 Z= 0.279 Chirality : 0.041 0.185 796 Planarity : 0.004 0.043 959 Dihedral : 3.991 14.748 715 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.99 % Allowed : 16.17 % Favored : 80.84 % 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: 1.30 (0.33), residues: 654 helix: 1.59 (0.30), residues: 293 sheet: 0.09 (0.55), residues: 74 loop : 0.45 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 176 HIS 0.006 0.001 HIS A 51 PHE 0.012 0.001 PHE A 278 TYR 0.009 0.001 TYR A 460 ARG 0.010 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.637 Fit side-chains REVERT: A 21 ARG cc_start: 0.7209 (tmt170) cc_final: 0.6832 (tpt170) REVERT: A 32 GLU cc_start: 0.8443 (pt0) cc_final: 0.8082 (pt0) REVERT: A 98 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8076 (ptp-110) REVERT: A 110 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 156 ARG cc_start: 0.7995 (ttp-110) cc_final: 0.7622 (ptm-80) REVERT: A 159 ASP cc_start: 0.8547 (m-30) cc_final: 0.8031 (m-30) REVERT: A 168 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7917 (mm-30) REVERT: A 219 ARG cc_start: 0.8149 (tmt-80) cc_final: 0.7465 (tpt90) REVERT: A 263 GLN cc_start: 0.7527 (mt0) cc_final: 0.7162 (mt0) REVERT: A 435 GLN cc_start: 0.8872 (tt0) cc_final: 0.8324 (mp10) REVERT: A 548 LEU cc_start: 0.8885 (tp) cc_final: 0.8631 (tm) REVERT: A 603 ASP cc_start: 0.8727 (t0) cc_final: 0.8106 (t0) REVERT: A 651 TYR cc_start: 0.8802 (m-80) cc_final: 0.8525 (m-10) outliers start: 17 outliers final: 7 residues processed: 75 average time/residue: 1.1356 time to fit residues: 89.1326 Evaluate side-chains 68 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 646 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 0.0470 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5428 Z= 0.219 Angle : 0.571 7.934 7378 Z= 0.277 Chirality : 0.041 0.182 796 Planarity : 0.004 0.043 959 Dihedral : 3.974 14.526 715 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.11 % Allowed : 17.05 % Favored : 80.84 % 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: 1.36 (0.33), residues: 654 helix: 1.64 (0.30), residues: 293 sheet: 0.07 (0.55), residues: 74 loop : 0.51 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 176 HIS 0.006 0.001 HIS A 51 PHE 0.010 0.001 PHE A 278 TYR 0.008 0.001 TYR A 460 ARG 0.010 0.000 ARG A 485 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1308 Ramachandran restraints generated. 654 Oldfield, 0 Emsley, 654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.631 Fit side-chains REVERT: A 32 GLU cc_start: 0.8439 (pt0) cc_final: 0.8069 (pt0) REVERT: A 98 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8064 (ptp-110) REVERT: A 110 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 156 ARG cc_start: 0.7981 (ttp-110) cc_final: 0.7634 (ptm-80) REVERT: A 158 ASP cc_start: 0.8354 (m-30) cc_final: 0.8005 (m-30) REVERT: A 159 ASP cc_start: 0.8549 (m-30) cc_final: 0.8017 (m-30) REVERT: A 168 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 219 ARG cc_start: 0.8152 (tmt-80) cc_final: 0.7444 (tpt170) REVERT: A 263 GLN cc_start: 0.7512 (mt0) cc_final: 0.7169 (mt0) REVERT: A 287 ASN cc_start: 0.8617 (t0) cc_final: 0.8276 (t0) REVERT: A 435 GLN cc_start: 0.8854 (tt0) cc_final: 0.8322 (mp10) REVERT: A 548 LEU cc_start: 0.8852 (tp) cc_final: 0.8589 (tm) REVERT: A 603 ASP cc_start: 0.8730 (t0) cc_final: 0.8111 (t0) REVERT: A 651 TYR cc_start: 0.8792 (m-80) cc_final: 0.8519 (m-10) outliers start: 12 outliers final: 7 residues processed: 72 average time/residue: 1.3371 time to fit residues: 100.4168 Evaluate side-chains 68 residues out of total 569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 646 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.102557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087951 restraints weight = 9762.217| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.74 r_work: 0.3149 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5428 Z= 0.237 Angle : 0.583 8.109 7378 Z= 0.281 Chirality : 0.041 0.182 796 Planarity : 0.004 0.043 959 Dihedral : 3.979 14.972 715 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.28 % Allowed : 16.87 % Favored : 80.84 % 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: 1.34 (0.33), residues: 654 helix: 1.63 (0.30), residues: 292 sheet: 0.04 (0.55), residues: 74 loop : 0.50 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 176 HIS 0.007 0.001 HIS A 51 PHE 0.011 0.001 PHE A 278 TYR 0.008 0.001 TYR A 460 ARG 0.012 0.001 ARG A 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2439.06 seconds wall clock time: 44 minutes 1.94 seconds (2641.94 seconds total)