Starting phenix.real_space_refine on Thu Sep 26 00:05:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/09_2024/6wcc_21606.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/09_2024/6wcc_21606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/09_2024/6wcc_21606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/09_2024/6wcc_21606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/09_2024/6wcc_21606.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wcc_21606/09_2024/6wcc_21606.cif" } resolution = 3.24 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 ------------------------------------------------------------------------------- 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= 1.000 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: 6 Type Number sf(0) Gaussians Cs 5 16.47 5 S 38 5.16 5 C 3758 2.51 5 N 940 2.21 5 O 980 1.98 5 H 5908 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11629 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5806 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5806 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 5.79, per 1000 atoms: 0.50 Number of scatterers: 11629 At special positions: 0 Unit cell: (107.712, 66.368, 78.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cs 5 54.66 S 38 16.00 O 980 8.00 N 940 7.00 C 3758 6.00 H 5908 1.00 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: 3.17 Conformation dependent library (CDL) restraints added in 934.8 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 86.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 67 through 103 removed outlier: 4.180A pdb=" N GLN A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 137 through 164 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 257 through 284 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 333 removed outlier: 3.839A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 3.624A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.544A pdb=" N ALA A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 400 removed outlier: 3.912A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 4.951A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'B' and resid 33 through 50 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 67 through 103 removed outlier: 4.180A pdb=" N GLN B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 137 through 164 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 257 through 284 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 298 through 333 removed outlier: 3.840A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 3.624A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.544A pdb=" N ALA B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 400 removed outlier: 3.912A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 4.952A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 462 hydrogen bonds defined for protein. 1368 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: 4.88 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5890 1.03 - 1.23: 18 1.23 - 1.42: 2386 1.42 - 1.61: 3394 1.61 - 1.81: 58 Bond restraints: 11746 Sorted by residual: bond pdb=" CG LEU B 470 " pdb=" CD1 LEU B 470 " ideal model delta sigma weight residual 1.521 1.559 -0.038 3.30e-02 9.18e+02 1.31e+00 bond pdb=" CG PHE A 295 " pdb=" CD2 PHE A 295 " ideal model delta sigma weight residual 1.384 1.360 0.024 2.10e-02 2.27e+03 1.26e+00 bond pdb=" CG LEU A 470 " pdb=" CD1 LEU A 470 " ideal model delta sigma weight residual 1.521 1.558 -0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CG PHE B 295 " pdb=" CD2 PHE B 295 " ideal model delta sigma weight residual 1.384 1.361 0.023 2.10e-02 2.27e+03 1.17e+00 bond pdb=" CB GLU B 59 " pdb=" CG GLU B 59 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.96e-01 ... (remaining 11741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 21172 2.12 - 4.24: 111 4.24 - 6.37: 8 6.37 - 8.49: 3 8.49 - 10.61: 2 Bond angle restraints: 21296 Sorted by residual: angle pdb=" CG LEU A 470 " pdb=" CD2 LEU A 470 " pdb="HD23 LEU A 470 " ideal model delta sigma weight residual 109.00 98.39 10.61 3.00e+00 1.11e-01 1.25e+01 angle pdb="HD21 LEU A 470 " pdb=" CD2 LEU A 470 " pdb="HD23 LEU A 470 " ideal model delta sigma weight residual 110.00 100.10 9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CG LEU A 470 " pdb=" CD2 LEU A 470 " pdb="HD21 LEU A 470 " ideal model delta sigma weight residual 109.00 117.41 -8.41 3.00e+00 1.11e-01 7.85e+00 angle pdb=" CD2 LEU B 470 " pdb=" CG LEU B 470 " pdb=" HG LEU B 470 " ideal model delta sigma weight residual 108.00 100.28 7.72 3.00e+00 1.11e-01 6.63e+00 angle pdb="HD22 LEU A 470 " pdb=" CD2 LEU A 470 " pdb="HD23 LEU A 470 " ideal model delta sigma weight residual 110.00 116.89 -6.89 3.00e+00 1.11e-01 5.28e+00 ... (remaining 21291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 4918 16.97 - 33.93: 428 33.93 - 50.90: 118 50.90 - 67.86: 58 67.86 - 84.83: 6 Dihedral angle restraints: 5528 sinusoidal: 2936 harmonic: 2592 Sorted by residual: dihedral pdb=" CA ASP A 283 " pdb=" C ASP A 283 " pdb=" N ASN A 284 " pdb=" CA ASN A 284 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP B 283 " pdb=" C ASP B 283 " pdb=" N ASN B 284 " pdb=" CA ASN B 284 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASN B 284 " pdb=" CB ASN B 284 " pdb=" CG ASN B 284 " pdb=" OD1 ASN B 284 " ideal model delta sinusoidal sigma weight residual -90.00 -162.72 72.72 2 2.00e+01 2.50e-03 1.09e+01 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 721 0.027 - 0.053: 128 0.053 - 0.080: 84 0.080 - 0.107: 34 0.107 - 0.134: 11 Chirality restraints: 978 Sorted by residual: chirality pdb=" CG LEU A 470 " pdb=" CB LEU A 470 " pdb=" CD1 LEU A 470 " pdb=" CD2 LEU A 470 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CG LEU B 470 " pdb=" CB LEU B 470 " pdb=" CD1 LEU B 470 " pdb=" CD2 LEU B 470 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL A 285 " pdb=" N VAL A 285 " pdb=" C VAL A 285 " pdb=" CB VAL A 285 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 975 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 295 " -0.028 2.00e-02 2.50e+03 1.82e-02 9.89e+00 pdb=" CG PHE A 295 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 295 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 295 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 295 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 295 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 295 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 295 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE A 295 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE A 295 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 295 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 295 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 295 " 0.022 2.00e-02 2.50e+03 1.78e-02 9.48e+00 pdb=" CG PHE B 295 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE B 295 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 295 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 295 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 295 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 295 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE B 295 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 295 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE B 295 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 295 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE B 295 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 123 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 124 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " -0.021 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.60: 12042 2.60 - 3.41: 46823 3.41 - 4.23: 62751 4.23 - 5.04: 110077 5.04 - 5.86: 145341 Nonbonded interactions: 377034 Sorted by model distance: nonbonded pdb=" O LEU B 123 " pdb=" HG1 THR B 126 " model vdw 1.784 2.450 nonbonded pdb=" O LEU A 123 " pdb=" HG1 THR A 126 " model vdw 1.784 2.450 nonbonded pdb=" OD1 ASP A 266 " pdb="HH21 ARG B 35 " model vdw 1.812 2.450 nonbonded pdb=" O ALA A 93 " pdb=" HG1 THR A 96 " model vdw 1.812 2.450 nonbonded pdb=" O ALA B 93 " pdb=" HG1 THR B 96 " model vdw 1.813 2.450 ... (remaining 377029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 476 or resid 701 through 702)) selection = chain 'B' } 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: 0.420 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: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.230 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.003 0.038 5838 Z= 0.170 Angle : 0.510 4.479 7956 Z= 0.278 Chirality : 0.033 0.134 978 Planarity : 0.004 0.038 976 Dihedral : 15.734 84.831 2040 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.26 % Allowed : 10.32 % Favored : 87.42 % 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: 1.46 (0.28), residues: 726 helix: 1.59 (0.19), residues: 590 sheet: None (None), residues: 0 loop : -1.76 (0.44), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 394 HIS 0.003 0.001 HIS B 328 PHE 0.053 0.001 PHE A 295 TYR 0.008 0.001 TYR A 313 ARG 0.001 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 ARG cc_start: 0.8477 (mtp180) cc_final: 0.8276 (mtp180) REVERT: B 335 ARG cc_start: 0.8501 (mtp180) cc_final: 0.8301 (mtp180) REVERT: B 418 LEU cc_start: 0.8247 (tp) cc_final: 0.7967 (mp) outliers start: 14 outliers final: 12 residues processed: 143 average time/residue: 0.3977 time to fit residues: 73.3026 Evaluate side-chains 104 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS B 113 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5838 Z= 0.254 Angle : 0.536 5.521 7956 Z= 0.273 Chirality : 0.036 0.128 978 Planarity : 0.004 0.045 976 Dihedral : 7.967 70.280 804 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.90 % Allowed : 14.03 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.30), residues: 726 helix: 2.84 (0.20), residues: 598 sheet: None (None), residues: 0 loop : -1.12 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 394 HIS 0.005 0.001 HIS A 328 PHE 0.018 0.002 PHE A 99 TYR 0.012 0.002 TYR A 313 ARG 0.003 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7585 (mmt) cc_final: 0.7259 (mmp) REVERT: B 117 MET cc_start: 0.7758 (mmp) cc_final: 0.7530 (mmt) REVERT: B 418 LEU cc_start: 0.8305 (tp) cc_final: 0.7878 (mp) outliers start: 18 outliers final: 16 residues processed: 121 average time/residue: 0.3892 time to fit residues: 61.8867 Evaluate side-chains 114 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 30.0000 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5838 Z= 0.278 Angle : 0.528 5.479 7956 Z= 0.273 Chirality : 0.036 0.136 978 Planarity : 0.004 0.049 976 Dihedral : 7.118 58.256 802 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.23 % Allowed : 14.52 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.31), residues: 726 helix: 3.11 (0.20), residues: 586 sheet: None (None), residues: 0 loop : -0.93 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.017 0.002 PHE A 99 TYR 0.014 0.002 TYR B 160 ARG 0.003 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.7892 (mmp) cc_final: 0.7631 (mmt) outliers start: 20 outliers final: 18 residues processed: 114 average time/residue: 0.3595 time to fit residues: 54.5857 Evaluate side-chains 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5838 Z= 0.242 Angle : 0.500 4.102 7956 Z= 0.258 Chirality : 0.035 0.124 978 Planarity : 0.004 0.045 976 Dihedral : 6.357 56.650 800 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.55 % Allowed : 15.00 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.72 (0.31), residues: 726 helix: 3.09 (0.20), residues: 598 sheet: None (None), residues: 0 loop : -0.92 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.004 0.001 HIS B 328 PHE 0.016 0.001 PHE B 99 TYR 0.012 0.002 TYR B 160 ARG 0.003 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.4549 (OUTLIER) cc_final: 0.4302 (tp) outliers start: 22 outliers final: 17 residues processed: 113 average time/residue: 0.3625 time to fit residues: 54.2909 Evaluate side-chains 112 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5838 Z= 0.410 Angle : 0.575 4.714 7956 Z= 0.305 Chirality : 0.038 0.142 978 Planarity : 0.005 0.044 976 Dihedral : 5.830 56.994 792 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.55 % Allowed : 15.97 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.30), residues: 726 helix: 2.70 (0.20), residues: 600 sheet: None (None), residues: 0 loop : -0.85 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.005 0.001 HIS B 328 PHE 0.018 0.002 PHE A 99 TYR 0.010 0.002 TYR B 426 ARG 0.005 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.880 Fit side-chains REVERT: A 381 THR cc_start: 0.9010 (m) cc_final: 0.8692 (p) REVERT: B 117 MET cc_start: 0.7637 (mmt) cc_final: 0.7419 (mmp) REVERT: B 381 THR cc_start: 0.9009 (m) cc_final: 0.8699 (p) outliers start: 22 outliers final: 17 residues processed: 111 average time/residue: 0.3565 time to fit residues: 52.5773 Evaluate side-chains 114 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 430 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5838 Z= 0.235 Angle : 0.497 4.074 7956 Z= 0.256 Chirality : 0.035 0.126 978 Planarity : 0.004 0.046 976 Dihedral : 5.278 56.185 790 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.74 % Allowed : 16.29 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.31), residues: 726 helix: 2.99 (0.20), residues: 602 sheet: None (None), residues: 0 loop : -0.87 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.004 0.001 HIS B 328 PHE 0.016 0.001 PHE A 99 TYR 0.010 0.002 TYR B 160 ARG 0.004 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.4164 (mm-30) cc_final: 0.3302 (mm-30) REVERT: B 282 GLU cc_start: 0.4163 (mm-30) cc_final: 0.3302 (mm-30) outliers start: 17 outliers final: 17 residues processed: 108 average time/residue: 0.3654 time to fit residues: 52.1177 Evaluate side-chains 111 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5838 Z= 0.200 Angle : 0.479 4.096 7956 Z= 0.246 Chirality : 0.034 0.123 978 Planarity : 0.004 0.045 976 Dihedral : 5.124 55.462 790 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.26 % Allowed : 16.77 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.31), residues: 726 helix: 3.25 (0.20), residues: 590 sheet: None (None), residues: 0 loop : -0.87 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 394 HIS 0.004 0.001 HIS B 328 PHE 0.014 0.001 PHE A 99 TYR 0.008 0.002 TYR A 313 ARG 0.003 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.4316 (mm-30) cc_final: 0.3530 (mm-30) REVERT: B 282 GLU cc_start: 0.4143 (mm-30) cc_final: 0.3304 (mm-30) outliers start: 14 outliers final: 14 residues processed: 103 average time/residue: 0.3741 time to fit residues: 51.0575 Evaluate side-chains 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5838 Z= 0.234 Angle : 0.495 5.010 7956 Z= 0.256 Chirality : 0.035 0.123 978 Planarity : 0.004 0.044 976 Dihedral : 5.029 55.467 788 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.26 % Allowed : 17.26 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.31), residues: 726 helix: 3.25 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -0.89 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.014 0.001 PHE A 99 TYR 0.008 0.002 TYR B 313 ARG 0.003 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.4356 (mm-30) cc_final: 0.3577 (mm-30) REVERT: B 282 GLU cc_start: 0.4179 (mm-30) cc_final: 0.3382 (mm-30) outliers start: 14 outliers final: 12 residues processed: 104 average time/residue: 0.3756 time to fit residues: 51.4170 Evaluate side-chains 105 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5838 Z= 0.197 Angle : 0.482 5.602 7956 Z= 0.247 Chirality : 0.034 0.121 978 Planarity : 0.004 0.045 976 Dihedral : 4.755 55.141 784 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.61 % Allowed : 18.23 % Favored : 80.16 % 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: 4.06 (0.31), residues: 726 helix: 3.32 (0.20), residues: 596 sheet: None (None), residues: 0 loop : -0.70 (0.54), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 394 HIS 0.003 0.001 HIS A 328 PHE 0.014 0.001 PHE B 99 TYR 0.008 0.002 TYR A 313 ARG 0.002 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.4442 (mm-30) cc_final: 0.3670 (mm-30) REVERT: B 282 GLU cc_start: 0.4284 (mm-30) cc_final: 0.3518 (mm-30) outliers start: 10 outliers final: 10 residues processed: 101 average time/residue: 0.3747 time to fit residues: 49.8566 Evaluate side-chains 104 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5838 Z= 0.185 Angle : 0.480 4.807 7956 Z= 0.245 Chirality : 0.034 0.121 978 Planarity : 0.004 0.045 976 Dihedral : 4.713 54.873 784 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.61 % Allowed : 18.39 % Favored : 80.00 % 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: 4.14 (0.31), residues: 726 helix: 3.38 (0.20), residues: 596 sheet: None (None), residues: 0 loop : -0.69 (0.54), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 394 HIS 0.003 0.001 HIS A 328 PHE 0.012 0.001 PHE B 99 TYR 0.008 0.002 TYR A 313 ARG 0.002 0.000 ARG B 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.4440 (mm-30) cc_final: 0.3671 (mm-30) REVERT: B 282 GLU cc_start: 0.4286 (mm-30) cc_final: 0.3520 (mm-30) outliers start: 10 outliers final: 8 residues processed: 104 average time/residue: 0.3918 time to fit residues: 54.4507 Evaluate side-chains 105 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 436 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.165492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.114608 restraints weight = 9904.370| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.69 r_work: 0.3002 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5838 Z= 0.254 Angle : 0.505 4.565 7956 Z= 0.261 Chirality : 0.035 0.123 978 Planarity : 0.004 0.044 976 Dihedral : 4.794 55.368 784 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.61 % Allowed : 18.55 % Favored : 79.84 % 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: 4.00 (0.31), residues: 726 helix: 3.28 (0.20), residues: 596 sheet: None (None), residues: 0 loop : -0.73 (0.54), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 394 HIS 0.004 0.001 HIS B 328 PHE 0.014 0.001 PHE B 99 TYR 0.009 0.002 TYR A 426 ARG 0.003 0.000 ARG B 35 =============================================================================== Job complete usr+sys time: 2748.79 seconds wall clock time: 49 minutes 2.63 seconds (2942.63 seconds total)