Starting phenix.real_space_refine on Tue Feb 11 02:20:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8edn_28037/02_2025/8edn_28037.cif Found real_map, /net/cci-nas-00/data/ceres_data/8edn_28037/02_2025/8edn_28037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8edn_28037/02_2025/8edn_28037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8edn_28037/02_2025/8edn_28037.map" model { file = "/net/cci-nas-00/data/ceres_data/8edn_28037/02_2025/8edn_28037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8edn_28037/02_2025/8edn_28037.cif" } resolution = 3.8 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= 0.003 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 13 5.16 5 C 2360 2.51 5 N 662 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3683 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 3683 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 21, 'TRANS': 557} Chain breaks: 8 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 977 Unresolved non-hydrogen angles: 1225 Unresolved non-hydrogen dihedrals: 770 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 22, 'TRP:plan': 1, 'ASP:plan': 24, 'PHE:plan': 7, 'GLU:plan': 30, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 485 Time building chain proxies: 3.08, per 1000 atoms: 0.84 Number of scatterers: 3683 At special positions: 0 Unit cell: (97.76, 80.08, 81.12, 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 13 16.00 O 648 8.00 N 662 7.00 C 2360 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 532.6 milliseconds 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1134 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 81.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 72 through 97 removed outlier: 4.121A pdb=" N GLU A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 105 removed outlier: 6.283A pdb=" N ARG A 103 " --> pdb=" O ASP A 100 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU A 104 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP A 105 " --> pdb=" O MET A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 130 through 147 removed outlier: 3.629A pdb=" N CYS A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 3.681A pdb=" N VAL A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.619A pdb=" N TYR A 182 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 205 through 227 removed outlier: 3.649A pdb=" N LYS A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.636A pdb=" N TYR A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 256 Processing helix chain 'A' and resid 259 through 276 Proline residue: A 268 - end of helix removed outlier: 3.554A pdb=" N ILE A 272 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.887A pdb=" N SER A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 293 through 308 Processing helix chain 'A' and resid 314 through 334 Processing helix chain 'A' and resid 341 through 358 removed outlier: 3.964A pdb=" N MET A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 387 Processing helix chain 'A' and resid 391 through 398 Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.545A pdb=" N PHE A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 503 Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.661A pdb=" N LEU A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.520A pdb=" N ALA A 542 " --> pdb=" O MET A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 565 through 588 Processing helix chain 'A' and resid 592 through 618 Processing helix chain 'A' and resid 678 through 697 removed outlier: 3.884A pdb=" N TRP A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 721 removed outlier: 4.479A pdb=" N LEU A 704 " --> pdb=" O THR A 700 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 945 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: 1.16 Time building geometry restraints manager: 1.16 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: 1249 1.34 - 1.46: 505 1.46 - 1.58: 1976 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3748 Sorted by residual: bond pdb=" N ARG A 304 " pdb=" CA ARG A 304 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.30e+00 bond pdb=" N ASP A 301 " pdb=" CA ASP A 301 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 6.08e+00 bond pdb=" N SER A 302 " pdb=" CA SER A 302 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.17e-02 7.31e+03 5.91e+00 bond pdb=" N LEU A 303 " pdb=" CA LEU A 303 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.16e-02 7.43e+03 5.58e+00 bond pdb=" N PHE A 299 " pdb=" CA PHE A 299 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.35e+00 ... (remaining 3743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 5118 2.52 - 5.03: 37 5.03 - 7.55: 3 7.55 - 10.07: 2 10.07 - 12.59: 1 Bond angle restraints: 5161 Sorted by residual: angle pdb=" C LYS A 305 " pdb=" N ALA A 306 " pdb=" CA ALA A 306 " ideal model delta sigma weight residual 120.38 112.49 7.89 1.46e+00 4.69e-01 2.92e+01 angle pdb=" N VAL A 432 " pdb=" CA VAL A 432 " pdb=" C VAL A 432 " ideal model delta sigma weight residual 113.47 108.34 5.13 1.01e+00 9.80e-01 2.58e+01 angle pdb=" CB MET A 546 " pdb=" CG MET A 546 " pdb=" SD MET A 546 " ideal model delta sigma weight residual 112.70 100.11 12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" CA LYS A 305 " pdb=" C LYS A 305 " pdb=" O LYS A 305 " ideal model delta sigma weight residual 121.07 116.94 4.13 1.10e+00 8.26e-01 1.41e+01 angle pdb=" CA LYS A 305 " pdb=" C LYS A 305 " pdb=" N ALA A 306 " ideal model delta sigma weight residual 116.79 120.98 -4.19 1.28e+00 6.10e-01 1.07e+01 ... (remaining 5156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.46: 1963 11.46 - 22.93: 148 22.93 - 34.39: 55 34.39 - 45.85: 17 45.85 - 57.31: 3 Dihedral angle restraints: 2186 sinusoidal: 472 harmonic: 1714 Sorted by residual: dihedral pdb=" CA LYS A 218 " pdb=" C LYS A 218 " pdb=" N ALA A 219 " pdb=" CA ALA A 219 " ideal model delta harmonic sigma weight residual 180.00 164.97 15.03 0 5.00e+00 4.00e-02 9.04e+00 dihedral pdb=" CA GLN A 576 " pdb=" CB GLN A 576 " pdb=" CG GLN A 576 " pdb=" CD GLN A 576 " ideal model delta sinusoidal sigma weight residual -60.00 -101.55 41.55 3 1.50e+01 4.44e-03 7.44e+00 dihedral pdb=" N PHE A 299 " pdb=" CA PHE A 299 " pdb=" CB PHE A 299 " pdb=" CG PHE A 299 " ideal model delta sinusoidal sigma weight residual 180.00 138.69 41.31 3 1.50e+01 4.44e-03 7.39e+00 ... (remaining 2183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 467 0.034 - 0.067: 140 0.067 - 0.101: 35 0.101 - 0.134: 6 0.134 - 0.168: 2 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA LEU A 300 " pdb=" N LEU A 300 " pdb=" C LEU A 300 " pdb=" CB LEU A 300 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA LEU A 303 " pdb=" N LEU A 303 " pdb=" C LEU A 303 " pdb=" CB LEU A 303 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA LYS A 305 " pdb=" N LYS A 305 " pdb=" C LYS A 305 " pdb=" CB LYS A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 647 not shown) Planarity restraints: 670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 218 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C LYS A 218 " 0.020 2.00e-02 2.50e+03 pdb=" O LYS A 218 " -0.007 2.00e-02 2.50e+03 pdb=" N ALA A 219 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 676 " 0.016 5.00e-02 4.00e+02 2.47e-02 9.80e-01 pdb=" N PRO A 677 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 677 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 677 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 677 " -0.016 5.00e-02 4.00e+02 2.41e-02 9.26e-01 pdb=" N PRO A 678 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 678 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 678 " -0.013 5.00e-02 4.00e+02 ... (remaining 667 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 364 2.74 - 3.28: 3962 3.28 - 3.82: 6422 3.82 - 4.36: 6359 4.36 - 4.90: 10953 Nonbonded interactions: 28060 Sorted by model distance: nonbonded pdb=" NH2 ARG A 440 " pdb=" O CYS A 509 " model vdw 2.205 3.120 nonbonded pdb=" O PHE A 443 " pdb=" OG1 THR A 446 " model vdw 2.246 3.040 nonbonded pdb=" O LYS A 584 " pdb=" OG SER A 587 " model vdw 2.312 3.040 nonbonded pdb=" NE2 HIS A 501 " pdb=" O GLU A 544 " model vdw 2.331 3.120 nonbonded pdb=" OH TYR A 235 " pdb=" O ILE A 275 " model vdw 2.346 3.040 ... (remaining 28055 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: 0.850 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.780 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 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 0.032 3748 Z= 0.168 Angle : 0.579 12.587 5161 Z= 0.342 Chirality : 0.036 0.168 650 Planarity : 0.003 0.029 670 Dihedral : 11.311 57.314 1052 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.70 % Favored : 94.12 % Rotamer: Outliers : 0.46 % Allowed : 0.92 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.37), residues: 561 helix: 2.78 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -1.19 (0.58), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 425 HIS 0.006 0.001 HIS A 393 PHE 0.016 0.001 PHE A 250 TYR 0.010 0.001 TYR A 408 ARG 0.002 0.001 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ASN cc_start: 0.8178 (t0) cc_final: 0.7626 (t0) REVERT: A 598 LYS cc_start: 0.8428 (mttm) cc_final: 0.8047 (mtpt) outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 0.1682 time to fit residues: 20.8658 Evaluate side-chains 50 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS A 510 ASN A 614 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.109088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.091660 restraints weight = 15142.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.093077 restraints weight = 11220.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.094119 restraints weight = 8936.788| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3748 Z= 0.178 Angle : 0.555 11.214 5161 Z= 0.288 Chirality : 0.036 0.153 650 Planarity : 0.007 0.139 670 Dihedral : 4.079 37.520 589 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.28 % Favored : 95.54 % Rotamer: Outliers : 2.76 % Allowed : 13.82 % Favored : 83.41 % 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: 2.64 (0.38), residues: 561 helix: 2.57 (0.25), residues: 438 sheet: None (None), residues: 0 loop : -1.46 (0.64), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.009 0.002 HIS A 588 PHE 0.031 0.003 PHE A 570 TYR 0.007 0.001 TYR A 333 ARG 0.008 0.001 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.485 Fit side-chains REVERT: A 408 TYR cc_start: 0.6547 (t80) cc_final: 0.6244 (t80) REVERT: A 579 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.6339 (t80) outliers start: 6 outliers final: 3 residues processed: 64 average time/residue: 0.1328 time to fit residues: 11.1218 Evaluate side-chains 51 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 579 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.0270 chunk 38 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS A 614 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.108832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.091210 restraints weight = 15143.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.092674 restraints weight = 10946.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.093577 restraints weight = 8571.296| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3748 Z= 0.141 Angle : 0.524 9.195 5161 Z= 0.272 Chirality : 0.035 0.130 650 Planarity : 0.005 0.081 670 Dihedral : 3.535 16.799 587 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.57 % Favored : 96.26 % Rotamer: Outliers : 4.15 % Allowed : 16.13 % Favored : 79.72 % 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: 2.63 (0.37), residues: 561 helix: 2.56 (0.24), residues: 444 sheet: None (None), residues: 0 loop : -1.72 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.006 0.001 HIS A 553 PHE 0.025 0.002 PHE A 579 TYR 0.006 0.001 TYR A 491 ARG 0.005 0.001 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 598 LYS cc_start: 0.8617 (mttt) cc_final: 0.8040 (mttp) REVERT: A 602 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7740 (mm-30) REVERT: A 684 GLN cc_start: 0.7987 (tp40) cc_final: 0.7766 (mm-40) outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 0.1431 time to fit residues: 12.3093 Evaluate side-chains 50 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 571 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.103825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.085875 restraints weight = 15701.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.087234 restraints weight = 11382.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.088238 restraints weight = 9055.722| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3748 Z= 0.225 Angle : 0.605 11.370 5161 Z= 0.317 Chirality : 0.038 0.160 650 Planarity : 0.004 0.040 670 Dihedral : 3.898 16.667 587 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.63 % Favored : 95.19 % Rotamer: Outliers : 4.61 % Allowed : 17.05 % Favored : 78.34 % 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: 2.27 (0.36), residues: 561 helix: 2.32 (0.25), residues: 444 sheet: None (None), residues: 0 loop : -1.85 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 599 HIS 0.007 0.001 HIS A 501 PHE 0.023 0.002 PHE A 570 TYR 0.018 0.002 TYR A 333 ARG 0.006 0.001 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.431 Fit side-chains REVERT: A 408 TYR cc_start: 0.7616 (t80) cc_final: 0.7389 (t80) outliers start: 10 outliers final: 5 residues processed: 60 average time/residue: 0.1400 time to fit residues: 10.7872 Evaluate side-chains 48 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 530 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.0670 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.103685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.086022 restraints weight = 15598.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.087443 restraints weight = 11126.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.088253 restraints weight = 8771.447| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3748 Z= 0.171 Angle : 0.572 12.490 5161 Z= 0.287 Chirality : 0.036 0.156 650 Planarity : 0.003 0.038 670 Dihedral : 3.669 15.416 587 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.28 % Favored : 95.54 % Rotamer: Outliers : 4.61 % Allowed : 20.28 % Favored : 75.12 % 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: 2.46 (0.37), residues: 561 helix: 2.46 (0.25), residues: 443 sheet: None (None), residues: 0 loop : -1.80 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 561 HIS 0.004 0.001 HIS A 588 PHE 0.016 0.001 PHE A 358 TYR 0.004 0.001 TYR A 333 ARG 0.004 0.001 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 ILE cc_start: 0.8776 (mm) cc_final: 0.8477 (mm) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 0.1146 time to fit residues: 8.5019 Evaluate side-chains 48 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.101677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.083837 restraints weight = 15585.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.085215 restraints weight = 11295.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.085932 restraints weight = 8973.652| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3748 Z= 0.199 Angle : 0.605 8.948 5161 Z= 0.309 Chirality : 0.036 0.125 650 Planarity : 0.004 0.039 670 Dihedral : 3.780 15.948 587 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.10 % Favored : 95.72 % Rotamer: Outliers : 5.07 % Allowed : 19.82 % Favored : 75.12 % 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: 2.39 (0.36), residues: 561 helix: 2.39 (0.24), residues: 439 sheet: None (None), residues: 0 loop : -1.59 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 561 HIS 0.005 0.001 HIS A 501 PHE 0.018 0.002 PHE A 358 TYR 0.012 0.002 TYR A 333 ARG 0.001 0.000 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 553 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.6344 (t-90) REVERT: A 573 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7716 (tp) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 0.1329 time to fit residues: 8.9565 Evaluate side-chains 47 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 553 HIS Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 600 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 HIS ** 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 = 0.3977 r_free = 0.3977 target = 0.101200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.083444 restraints weight = 15586.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.084761 restraints weight = 11399.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.085770 restraints weight = 9126.043| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.7682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3748 Z= 0.181 Angle : 0.571 7.784 5161 Z= 0.295 Chirality : 0.035 0.117 650 Planarity : 0.004 0.038 670 Dihedral : 3.777 18.267 587 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 4.61 % Allowed : 19.35 % Favored : 76.04 % 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: 2.45 (0.37), residues: 561 helix: 2.41 (0.25), residues: 445 sheet: None (None), residues: 0 loop : -1.67 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 267 HIS 0.004 0.001 HIS A 501 PHE 0.024 0.002 PHE A 358 TYR 0.010 0.001 TYR A 408 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.8377 (m110) cc_final: 0.8094 (m-40) REVERT: A 553 HIS cc_start: 0.7230 (OUTLIER) cc_final: 0.6369 (t-90) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.1449 time to fit residues: 9.7175 Evaluate side-chains 47 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 553 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 32 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 HIS ** 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 = 0.3978 r_free = 0.3978 target = 0.101075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.083328 restraints weight = 15736.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.084814 restraints weight = 11182.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.085938 restraints weight = 8790.294| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.7997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3748 Z= 0.144 Angle : 0.529 7.726 5161 Z= 0.275 Chirality : 0.035 0.116 650 Planarity : 0.003 0.041 670 Dihedral : 3.576 16.238 587 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.10 % Favored : 95.72 % Rotamer: Outliers : 4.15 % Allowed : 20.28 % Favored : 75.58 % 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: 2.61 (0.37), residues: 561 helix: 2.53 (0.25), residues: 445 sheet: None (None), residues: 0 loop : -1.62 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 267 HIS 0.004 0.001 HIS A 588 PHE 0.020 0.001 PHE A 579 TYR 0.009 0.001 TYR A 408 ARG 0.002 0.000 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 222 ASN cc_start: 0.8411 (m110) cc_final: 0.8057 (m-40) REVERT: A 553 HIS cc_start: 0.7420 (OUTLIER) cc_final: 0.6584 (t-90) outliers start: 9 outliers final: 7 residues processed: 47 average time/residue: 0.1156 time to fit residues: 7.4802 Evaluate side-chains 47 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 553 HIS Chi-restraints excluded: chain A residue 693 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 HIS ** 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 = 0.3930 r_free = 0.3930 target = 0.098110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.081054 restraints weight = 15736.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.082434 restraints weight = 11393.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.083424 restraints weight = 8991.896| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.8934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3748 Z= 0.207 Angle : 0.574 9.296 5161 Z= 0.302 Chirality : 0.036 0.119 650 Planarity : 0.004 0.045 670 Dihedral : 3.892 17.174 587 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.28 % Favored : 95.54 % Rotamer: Outliers : 4.15 % Allowed : 21.66 % Favored : 74.19 % 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: 2.31 (0.36), residues: 561 helix: 2.39 (0.25), residues: 439 sheet: None (None), residues: 0 loop : -1.87 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 571 HIS 0.007 0.001 HIS A 501 PHE 0.029 0.002 PHE A 579 TYR 0.016 0.002 TYR A 408 ARG 0.004 0.001 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.368 Fit side-chains REVERT: A 553 HIS cc_start: 0.7167 (OUTLIER) cc_final: 0.6460 (t-90) REVERT: A 571 TRP cc_start: 0.6263 (m-10) cc_final: 0.5929 (m-10) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.1149 time to fit residues: 7.5993 Evaluate side-chains 45 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 553 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 14 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 0.0000 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** 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 = 0.3954 r_free = 0.3954 target = 0.099081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.082361 restraints weight = 15768.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.083778 restraints weight = 11209.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.084824 restraints weight = 8743.366| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.9136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3748 Z= 0.156 Angle : 0.539 8.153 5161 Z= 0.280 Chirality : 0.035 0.116 650 Planarity : 0.004 0.047 670 Dihedral : 3.644 16.191 587 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 2.76 % Allowed : 22.58 % Favored : 74.65 % 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: 2.58 (0.37), residues: 561 helix: 2.49 (0.25), residues: 445 sheet: None (None), residues: 0 loop : -1.58 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 561 HIS 0.004 0.001 HIS A 501 PHE 0.022 0.002 PHE A 579 TYR 0.008 0.001 TYR A 227 ARG 0.002 0.000 ARG A 607 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1122 Ramachandran restraints generated. 561 Oldfield, 0 Emsley, 561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.440 Fit side-chains REVERT: A 553 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6336 (t-90) outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 0.1162 time to fit residues: 7.1889 Evaluate side-chains 40 residues out of total 526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 553 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.0010 chunk 7 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 HIS ** 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 = 0.3937 r_free = 0.3937 target = 0.098308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.081368 restraints weight = 15972.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.082763 restraints weight = 11447.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.083731 restraints weight = 8980.936| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.9475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3748 Z= 0.163 Angle : 0.553 8.390 5161 Z= 0.293 Chirality : 0.035 0.195 650 Planarity : 0.003 0.029 670 Dihedral : 3.657 16.107 587 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.10 % Favored : 95.72 % Rotamer: Outliers : 3.23 % Allowed : 21.20 % Favored : 75.58 % 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: 2.55 (0.37), residues: 561 helix: 2.48 (0.25), residues: 445 sheet: None (None), residues: 0 loop : -1.62 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 561 HIS 0.005 0.001 HIS A 501 PHE 0.024 0.002 PHE A 579 TYR 0.026 0.002 TYR A 408 ARG 0.004 0.001 ARG A 681 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1321.61 seconds wall clock time: 24 minutes 15.64 seconds (1455.64 seconds total)