Starting phenix.real_space_refine on Fri Apr 5 19:32:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iva_35755/04_2024/8iva_35755.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iva_35755/04_2024/8iva_35755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iva_35755/04_2024/8iva_35755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iva_35755/04_2024/8iva_35755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iva_35755/04_2024/8iva_35755.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iva_35755/04_2024/8iva_35755.pdb" } resolution = 3.95 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= 0.010 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 26 5.16 5 C 3182 2.51 5 N 827 2.21 5 O 994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 357": "NH1" <-> "NH2" Residue "G ARG 408": "NH1" <-> "NH2" Residue "H GLU 1": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5029 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.20, per 1000 atoms: 0.64 Number of scatterers: 5029 At special positions: 0 Unit cell: (80.912, 77.8, 108.142, 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 26 16.00 O 994 8.00 N 827 7.00 C 3182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.28 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.01 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 940.5 milliseconds 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 15 sheets defined 5.6% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.529A pdb=" N ALA G 352 " --> pdb=" O SER G 349 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 349 through 353' Processing helix chain 'G' and resid 364 through 370 removed outlier: 3.868A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.130A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.695A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.669A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.140A pdb=" N GLY C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 50 removed outlier: 4.834A pdb=" N TYR C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ARG C 38 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS C 35 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.617A pdb=" N THR E 72 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 11 removed outlier: 4.037A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 44 through 46 Processing sheet with id=AA7, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'G' and resid 354 through 358 removed outlier: 3.696A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'L' and resid 19 through 29 removed outlier: 3.829A pdb=" N VAL L 25 " --> pdb=" O THR L 68 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR L 68 " --> pdb=" O VAL L 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.789A pdb=" N TRP L 34 " --> pdb=" O PHE L 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.124A pdb=" N MET H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER H 25 " --> pdb=" O MET H 3 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR H 80 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.595A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.595A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 324 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: 1.24 Time building geometry restraints manager: 1.98 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: 1558 1.34 - 1.46: 1395 1.46 - 1.58: 2165 1.58 - 1.71: 0 1.71 - 1.83: 36 Bond restraints: 5154 Sorted by residual: bond pdb=" CA ALA G 475 " pdb=" C ALA G 475 " ideal model delta sigma weight residual 1.522 1.571 -0.049 9.30e-03 1.16e+04 2.75e+01 bond pdb=" N ASP G 442 " pdb=" CA ASP G 442 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.16e-02 7.43e+03 1.04e+01 bond pdb=" N TYR G 473 " pdb=" CA TYR G 473 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.24e+00 bond pdb=" N GLN G 474 " pdb=" CA GLN G 474 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.29e-02 6.01e+03 9.15e+00 bond pdb=" N ALA G 475 " pdb=" CA ALA G 475 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.15e-02 7.56e+03 9.09e+00 ... (remaining 5149 not shown) Histogram of bond angle deviations from ideal: 100.06 - 107.14: 159 107.14 - 114.22: 2813 114.22 - 121.31: 2561 121.31 - 128.39: 1425 128.39 - 135.47: 43 Bond angle restraints: 7001 Sorted by residual: angle pdb=" C LEU G 335 " pdb=" N CYS G 336 " pdb=" CA CYS G 336 " ideal model delta sigma weight residual 120.49 135.47 -14.98 1.42e+00 4.96e-01 1.11e+02 angle pdb=" N ALA G 475 " pdb=" CA ALA G 475 " pdb=" C ALA G 475 " ideal model delta sigma weight residual 112.12 124.69 -12.57 1.34e+00 5.57e-01 8.80e+01 angle pdb=" N SER G 477 " pdb=" CA SER G 477 " pdb=" C SER G 477 " ideal model delta sigma weight residual 112.38 123.66 -11.28 1.22e+00 6.72e-01 8.55e+01 angle pdb=" N CYS G 480 " pdb=" CA CYS G 480 " pdb=" C CYS G 480 " ideal model delta sigma weight residual 112.45 121.62 -9.17 1.39e+00 5.18e-01 4.35e+01 angle pdb=" N LEU G 441 " pdb=" CA LEU G 441 " pdb=" C LEU G 441 " ideal model delta sigma weight residual 111.36 117.78 -6.42 1.09e+00 8.42e-01 3.47e+01 ... (remaining 6996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 2735 17.75 - 35.50: 250 35.50 - 53.25: 46 53.25 - 71.00: 4 71.00 - 88.75: 5 Dihedral angle restraints: 3040 sinusoidal: 1179 harmonic: 1861 Sorted by residual: dihedral pdb=" CB CYS G 391 " pdb=" SG CYS G 391 " pdb=" SG CYS G 525 " pdb=" CB CYS G 525 " ideal model delta sinusoidal sigma weight residual 93.00 46.06 46.94 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CA LEU G 461 " pdb=" C LEU G 461 " pdb=" N LYS G 462 " pdb=" CA LYS G 462 " ideal model delta harmonic sigma weight residual 180.00 157.06 22.94 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA TRP L 90 " pdb=" C TRP L 90 " pdb=" N SER L 91 " pdb=" CA SER L 91 " ideal model delta harmonic sigma weight residual -180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 3037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 654 0.086 - 0.172: 94 0.172 - 0.258: 10 0.258 - 0.343: 2 0.343 - 0.429: 3 Chirality restraints: 763 Sorted by residual: chirality pdb=" CA ALA G 475 " pdb=" N ALA G 475 " pdb=" C ALA G 475 " pdb=" CB ALA G 475 " both_signs ideal model delta sigma weight residual False 2.48 2.06 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA CYS G 480 " pdb=" N CYS G 480 " pdb=" C CYS G 480 " pdb=" CB CYS G 480 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA SER G 477 " pdb=" N SER G 477 " pdb=" C SER G 477 " pdb=" CB SER G 477 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 760 not shown) Planarity restraints: 892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 94 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO E 95 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 472 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C ILE G 472 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE G 472 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR G 473 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR H 40 " -0.043 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO H 41 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " -0.036 5.00e-02 4.00e+02 ... (remaining 889 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1604 2.82 - 3.34: 4003 3.34 - 3.86: 8000 3.86 - 4.38: 8740 4.38 - 4.90: 15568 Nonbonded interactions: 37915 Sorted by model distance: nonbonded pdb=" O TYR E 49 " pdb=" OG SER E 53 " model vdw 2.302 2.440 nonbonded pdb=" O VAL L 29 " pdb=" OH TYR L 70 " model vdw 2.324 2.440 nonbonded pdb=" OH TYR L 86 " pdb=" O LYS H 43 " model vdw 2.349 2.440 nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.355 2.440 nonbonded pdb=" NE2 GLN E 6 " pdb=" OG1 THR E 102 " model vdw 2.378 2.520 ... (remaining 37910 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=0.50 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: 9.880 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: 38.810 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.920 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 5154 Z= 0.356 Angle : 0.974 14.984 7001 Z= 0.600 Chirality : 0.066 0.429 763 Planarity : 0.007 0.071 891 Dihedral : 13.804 88.750 1840 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.54 % Allowed : 7.43 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -4.03 (0.28), residues: 638 helix: -5.15 (0.31), residues: 14 sheet: -2.71 (0.30), residues: 223 loop : -2.65 (0.26), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 106 HIS 0.004 0.001 HIS C 35 PHE 0.022 0.002 PHE E 83 TYR 0.027 0.002 TYR E 94 ARG 0.005 0.001 ARG G 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 201 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7986 (ptm-80) REVERT: C 97 VAL cc_start: 0.8206 (m) cc_final: 0.7978 (m) REVERT: E 23 CYS cc_start: 0.7962 (t) cc_final: 0.7397 (t) REVERT: E 24 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7403 (ttm110) REVERT: E 27 GLN cc_start: 0.8312 (tt0) cc_final: 0.7881 (mp10) REVERT: E 42 LYS cc_start: 0.8276 (pttm) cc_final: 0.7935 (mtpt) REVERT: E 61 ARG cc_start: 0.7920 (ptt-90) cc_final: 0.7319 (ptt90) REVERT: E 82 ASP cc_start: 0.8556 (m-30) cc_final: 0.7458 (m-30) REVERT: E 89 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7478 (tm-30) REVERT: E 90 GLN cc_start: 0.7556 (pp30) cc_final: 0.6812 (pp30) REVERT: E 93 SER cc_start: 0.8477 (m) cc_final: 0.8133 (m) REVERT: E 107 LYS cc_start: 0.4448 (tttt) cc_final: 0.3688 (tptm) REVERT: G 335 LEU cc_start: 0.8075 (mp) cc_final: 0.7866 (mt) REVERT: G 369 TYR cc_start: 0.9026 (t80) cc_final: 0.8627 (t80) REVERT: G 378 LYS cc_start: 0.6890 (mttm) cc_final: 0.6514 (mtmm) REVERT: G 442 ASP cc_start: 0.8632 (m-30) cc_final: 0.8398 (m-30) REVERT: G 465 GLU cc_start: 0.8580 (tt0) cc_final: 0.8214 (tt0) REVERT: G 471 GLU cc_start: 0.8086 (tt0) cc_final: 0.7696 (pt0) REVERT: L 1 GLN cc_start: 0.8967 (pt0) cc_final: 0.8651 (pp30) REVERT: L 31 ASP cc_start: 0.7177 (p0) cc_final: 0.6598 (p0) REVERT: L 32 MET cc_start: 0.8278 (tpp) cc_final: 0.7996 (mmm) REVERT: L 34 TRP cc_start: 0.8514 (m100) cc_final: 0.7779 (m100) REVERT: L 44 LYS cc_start: 0.7328 (mtmm) cc_final: 0.6983 (ttpt) REVERT: L 86 TYR cc_start: 0.8370 (m-80) cc_final: 0.7987 (m-10) REVERT: H 19 LYS cc_start: 0.8173 (tttt) cc_final: 0.7585 (ptmt) REVERT: H 73 ASP cc_start: 0.7287 (t0) cc_final: 0.6969 (t0) REVERT: H 76 MET cc_start: 0.7944 (mpp) cc_final: 0.7696 (mtm) REVERT: H 93 MET cc_start: 0.6600 (tpp) cc_final: 0.6290 (tpp) REVERT: H 102 ASN cc_start: 0.8301 (p0) cc_final: 0.8001 (p0) REVERT: H 107 VAL cc_start: 0.8477 (p) cc_final: 0.8157 (t) outliers start: 3 outliers final: 0 residues processed: 204 average time/residue: 0.2051 time to fit residues: 50.9625 Evaluate side-chains 159 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 102 GLN G 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5154 Z= 0.225 Angle : 0.634 7.217 7001 Z= 0.341 Chirality : 0.046 0.172 763 Planarity : 0.005 0.055 891 Dihedral : 6.140 73.458 754 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.53 % Allowed : 16.12 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -3.38 (0.29), residues: 638 helix: -3.46 (0.81), residues: 21 sheet: -1.86 (0.33), residues: 219 loop : -2.50 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 106 HIS 0.003 0.001 HIS C 35 PHE 0.022 0.002 PHE G 400 TYR 0.024 0.002 TYR E 94 ARG 0.005 0.001 ARG G 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ARG cc_start: 0.8441 (ttm170) cc_final: 0.7998 (ttp80) REVERT: C 43 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8626 (mmmt) REVERT: C 87 ARG cc_start: 0.7512 (mtp-110) cc_final: 0.7213 (mtp-110) REVERT: C 89 GLU cc_start: 0.7826 (mp0) cc_final: 0.7414 (mp0) REVERT: C 94 TYR cc_start: 0.7859 (m-80) cc_final: 0.6947 (m-10) REVERT: E 18 ARG cc_start: 0.8547 (mtp-110) cc_final: 0.8246 (mmm-85) REVERT: E 24 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7557 (ttm110) REVERT: E 27 GLN cc_start: 0.8434 (tt0) cc_final: 0.7981 (mp10) REVERT: E 42 LYS cc_start: 0.8248 (pttm) cc_final: 0.7943 (mtpt) REVERT: E 82 ASP cc_start: 0.8569 (m-30) cc_final: 0.8174 (m-30) REVERT: E 89 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7180 (tm-30) REVERT: E 90 GLN cc_start: 0.7543 (pp30) cc_final: 0.7170 (pp30) REVERT: E 93 SER cc_start: 0.8346 (m) cc_final: 0.8052 (m) REVERT: E 107 LYS cc_start: 0.4464 (tttt) cc_final: 0.3940 (tptm) REVERT: G 369 TYR cc_start: 0.9098 (t80) cc_final: 0.8645 (t80) REVERT: G 378 LYS cc_start: 0.6862 (mttm) cc_final: 0.6465 (mtmm) REVERT: G 457 ARG cc_start: 0.7865 (ttt-90) cc_final: 0.7578 (ttt-90) REVERT: G 465 GLU cc_start: 0.8587 (tt0) cc_final: 0.8339 (tt0) REVERT: G 471 GLU cc_start: 0.8002 (tt0) cc_final: 0.7657 (pt0) REVERT: L 1 GLN cc_start: 0.8911 (pt0) cc_final: 0.8662 (pp30) REVERT: L 34 TRP cc_start: 0.8249 (m100) cc_final: 0.7273 (m100) REVERT: L 44 LYS cc_start: 0.7075 (mtmm) cc_final: 0.6732 (ttpt) REVERT: L 78 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7912 (mm-30) REVERT: L 86 TYR cc_start: 0.8292 (m-80) cc_final: 0.7826 (m-10) REVERT: H 73 ASP cc_start: 0.7174 (t0) cc_final: 0.6720 (t0) REVERT: H 76 MET cc_start: 0.8002 (mpp) cc_final: 0.7690 (mtm) REVERT: H 97 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8888 (p) REVERT: H 102 ASN cc_start: 0.8261 (p0) cc_final: 0.7935 (p0) outliers start: 25 outliers final: 14 residues processed: 184 average time/residue: 0.1824 time to fit residues: 42.0044 Evaluate side-chains 174 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 5154 Z= 0.152 Angle : 0.590 7.665 7001 Z= 0.315 Chirality : 0.044 0.156 763 Planarity : 0.005 0.054 891 Dihedral : 5.628 71.299 754 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.17 % Allowed : 20.47 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.98 (0.31), residues: 638 helix: -3.14 (0.92), residues: 21 sheet: -1.60 (0.34), residues: 225 loop : -2.21 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.001 0.000 HIS L 33 PHE 0.017 0.001 PHE G 400 TYR 0.020 0.001 TYR G 473 ARG 0.004 0.000 ARG G 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8519 (mmmt) REVERT: C 59 TYR cc_start: 0.8368 (t80) cc_final: 0.8104 (t80) REVERT: C 80 TYR cc_start: 0.7241 (m-10) cc_final: 0.6935 (m-10) REVERT: C 83 MET cc_start: 0.7741 (mtt) cc_final: 0.7229 (mtt) REVERT: E 24 ARG cc_start: 0.7774 (ttp-110) cc_final: 0.7490 (ttm110) REVERT: E 27 GLN cc_start: 0.8452 (tt0) cc_final: 0.8035 (mp10) REVERT: E 42 LYS cc_start: 0.8225 (pttm) cc_final: 0.7975 (mtpt) REVERT: E 82 ASP cc_start: 0.8683 (m-30) cc_final: 0.8308 (m-30) REVERT: E 90 GLN cc_start: 0.7731 (pp30) cc_final: 0.7349 (pp30) REVERT: E 107 LYS cc_start: 0.4387 (tttt) cc_final: 0.3724 (tptm) REVERT: G 340 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8466 (mp0) REVERT: G 369 TYR cc_start: 0.9061 (t80) cc_final: 0.8532 (t80) REVERT: G 378 LYS cc_start: 0.6895 (mttm) cc_final: 0.6486 (mtmm) REVERT: G 465 GLU cc_start: 0.8505 (tt0) cc_final: 0.8262 (tt0) REVERT: G 471 GLU cc_start: 0.8122 (tt0) cc_final: 0.7591 (pt0) REVERT: L 1 GLN cc_start: 0.8949 (pt0) cc_final: 0.8699 (pp30) REVERT: L 31 ASP cc_start: 0.7218 (p0) cc_final: 0.6959 (p0) REVERT: L 78 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7823 (mm-30) REVERT: H 73 ASP cc_start: 0.7139 (t0) cc_final: 0.6690 (t0) REVERT: H 76 MET cc_start: 0.8017 (mpp) cc_final: 0.7723 (mtm) REVERT: H 102 ASN cc_start: 0.8262 (p0) cc_final: 0.7950 (p0) outliers start: 23 outliers final: 17 residues processed: 171 average time/residue: 0.2048 time to fit residues: 43.7309 Evaluate side-chains 162 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.0030 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 0.0670 chunk 6 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.2446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5154 Z= 0.141 Angle : 0.587 8.286 7001 Z= 0.308 Chirality : 0.044 0.148 763 Planarity : 0.004 0.050 891 Dihedral : 5.347 70.434 754 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.89 % Allowed : 21.92 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.70 (0.31), residues: 638 helix: -3.37 (0.73), residues: 33 sheet: -1.26 (0.34), residues: 221 loop : -2.03 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.001 0.000 HIS C 99 PHE 0.020 0.001 PHE L 46 TYR 0.021 0.001 TYR G 473 ARG 0.006 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.7929 (mtm) cc_final: 0.6978 (ptm) REVERT: C 43 LYS cc_start: 0.8768 (mmtm) cc_final: 0.8512 (mmmt) REVERT: C 59 TYR cc_start: 0.8329 (t80) cc_final: 0.8069 (t80) REVERT: C 94 TYR cc_start: 0.7775 (m-80) cc_final: 0.6871 (m-10) REVERT: C 101 GLN cc_start: 0.8504 (mt0) cc_final: 0.8202 (mt0) REVERT: E 24 ARG cc_start: 0.7760 (ttp-110) cc_final: 0.7442 (ttm110) REVERT: E 27 GLN cc_start: 0.8489 (tt0) cc_final: 0.8061 (mp10) REVERT: E 42 LYS cc_start: 0.8228 (pttm) cc_final: 0.7959 (mtpt) REVERT: E 82 ASP cc_start: 0.8691 (m-30) cc_final: 0.8311 (m-30) REVERT: E 89 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: E 90 GLN cc_start: 0.7980 (pp30) cc_final: 0.7389 (pp30) REVERT: E 107 LYS cc_start: 0.4338 (tttt) cc_final: 0.3629 (tptm) REVERT: G 340 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8469 (mp0) REVERT: G 353 TRP cc_start: 0.7774 (p-90) cc_final: 0.7227 (p-90) REVERT: G 369 TYR cc_start: 0.9057 (t80) cc_final: 0.8512 (t80) REVERT: G 378 LYS cc_start: 0.6865 (mttm) cc_final: 0.6458 (mtmm) REVERT: G 457 ARG cc_start: 0.8141 (ttt-90) cc_final: 0.7273 (ttt-90) REVERT: G 465 GLU cc_start: 0.8477 (tt0) cc_final: 0.8199 (tt0) REVERT: G 471 GLU cc_start: 0.8100 (tt0) cc_final: 0.7582 (pt0) REVERT: L 1 GLN cc_start: 0.8959 (pt0) cc_final: 0.8717 (pp30) REVERT: L 78 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7804 (mm-30) REVERT: L 90 TRP cc_start: 0.8235 (t60) cc_final: 0.7824 (t60) REVERT: H 73 ASP cc_start: 0.7159 (t0) cc_final: 0.6107 (t0) REVERT: H 76 MET cc_start: 0.8013 (mpp) cc_final: 0.7431 (mpp) REVERT: H 98 ARG cc_start: 0.6594 (ttt180) cc_final: 0.6321 (ttt-90) REVERT: H 102 ASN cc_start: 0.8287 (p0) cc_final: 0.8008 (p0) outliers start: 27 outliers final: 17 residues processed: 174 average time/residue: 0.1871 time to fit residues: 40.5055 Evaluate side-chains 166 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN E 89 GLN G 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5154 Z= 0.283 Angle : 0.643 7.908 7001 Z= 0.338 Chirality : 0.046 0.181 763 Planarity : 0.005 0.055 891 Dihedral : 5.527 73.432 754 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 5.25 % Allowed : 20.83 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.68 (0.31), residues: 638 helix: -3.42 (0.80), residues: 27 sheet: -1.33 (0.34), residues: 231 loop : -1.98 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 106 HIS 0.003 0.001 HIS L 88 PHE 0.022 0.002 PHE G 377 TYR 0.021 0.002 TYR E 94 ARG 0.007 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8466 (mmmt) REVERT: C 59 TYR cc_start: 0.8276 (t80) cc_final: 0.7961 (t80) REVERT: C 73 ASP cc_start: 0.7012 (t70) cc_final: 0.6212 (t70) REVERT: C 76 LYS cc_start: 0.8527 (mmtm) cc_final: 0.8320 (mmtm) REVERT: C 89 GLU cc_start: 0.7719 (mp0) cc_final: 0.7172 (mp0) REVERT: C 98 LYS cc_start: 0.7400 (tmmt) cc_final: 0.7062 (tttm) REVERT: C 99 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.7569 (m-70) REVERT: C 101 GLN cc_start: 0.8403 (mt0) cc_final: 0.8196 (mt0) REVERT: E 24 ARG cc_start: 0.7607 (ttp-110) cc_final: 0.6837 (ttm170) REVERT: E 27 GLN cc_start: 0.8451 (tt0) cc_final: 0.8030 (mp10) REVERT: E 42 LYS cc_start: 0.8202 (pttm) cc_final: 0.7971 (mtpt) REVERT: E 82 ASP cc_start: 0.8628 (m-30) cc_final: 0.8248 (m-30) REVERT: E 89 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7863 (pp30) REVERT: E 90 GLN cc_start: 0.7882 (pp30) cc_final: 0.7380 (pp30) REVERT: G 340 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8488 (mp0) REVERT: G 353 TRP cc_start: 0.7978 (p-90) cc_final: 0.7510 (p-90) REVERT: G 369 TYR cc_start: 0.9082 (t80) cc_final: 0.8484 (t80) REVERT: G 465 GLU cc_start: 0.8519 (tt0) cc_final: 0.8236 (tt0) REVERT: G 471 GLU cc_start: 0.8087 (tt0) cc_final: 0.7535 (pt0) REVERT: L 1 GLN cc_start: 0.8939 (pt0) cc_final: 0.8708 (pp30) REVERT: L 44 LYS cc_start: 0.6998 (mtmm) cc_final: 0.6693 (ttpt) REVERT: H 73 ASP cc_start: 0.7164 (t0) cc_final: 0.6098 (t0) REVERT: H 76 MET cc_start: 0.8081 (mpp) cc_final: 0.7485 (mpp) REVERT: H 102 ASN cc_start: 0.8327 (p0) cc_final: 0.8049 (p0) outliers start: 29 outliers final: 21 residues processed: 157 average time/residue: 0.1954 time to fit residues: 38.1664 Evaluate side-chains 158 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5154 Z= 0.215 Angle : 0.633 7.970 7001 Z= 0.332 Chirality : 0.046 0.170 763 Planarity : 0.004 0.053 891 Dihedral : 5.544 74.381 754 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.25 % Allowed : 21.92 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.53 (0.31), residues: 638 helix: -3.47 (0.68), residues: 33 sheet: -1.06 (0.35), residues: 214 loop : -1.93 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 90 HIS 0.002 0.001 HIS L 88 PHE 0.017 0.002 PHE G 347 TYR 0.019 0.002 TYR E 94 ARG 0.008 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 GLU cc_start: 0.6228 (mp0) cc_final: 0.6000 (mp0) REVERT: C 43 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8480 (mmmt) REVERT: C 73 ASP cc_start: 0.7032 (t70) cc_final: 0.6182 (t70) REVERT: C 76 LYS cc_start: 0.8518 (mmtm) cc_final: 0.8281 (mmtm) REVERT: C 89 GLU cc_start: 0.7731 (mp0) cc_final: 0.7173 (mp0) REVERT: E 24 ARG cc_start: 0.7535 (ttp-110) cc_final: 0.6771 (ttm110) REVERT: E 27 GLN cc_start: 0.8451 (tt0) cc_final: 0.8018 (mp10) REVERT: E 82 ASP cc_start: 0.8628 (m-30) cc_final: 0.8242 (m-30) REVERT: E 89 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: E 90 GLN cc_start: 0.7757 (pp30) cc_final: 0.7121 (pp30) REVERT: G 340 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8472 (mp0) REVERT: G 353 TRP cc_start: 0.7998 (p-90) cc_final: 0.7504 (p-90) REVERT: G 369 TYR cc_start: 0.9055 (t80) cc_final: 0.8461 (t80) REVERT: G 457 ARG cc_start: 0.8230 (ttt-90) cc_final: 0.7697 (ttt-90) REVERT: G 462 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7482 (mtmm) REVERT: G 465 GLU cc_start: 0.8435 (tt0) cc_final: 0.8035 (tt0) REVERT: G 471 GLU cc_start: 0.8049 (tt0) cc_final: 0.7508 (pt0) REVERT: L 1 GLN cc_start: 0.8938 (pt0) cc_final: 0.8716 (pp30) REVERT: L 44 LYS cc_start: 0.6989 (mtmm) cc_final: 0.6679 (ttpt) REVERT: H 73 ASP cc_start: 0.7238 (t0) cc_final: 0.6068 (t0) REVERT: H 76 MET cc_start: 0.8056 (mpp) cc_final: 0.7400 (mpp) REVERT: H 78 THR cc_start: 0.6075 (OUTLIER) cc_final: 0.5530 (t) outliers start: 29 outliers final: 23 residues processed: 158 average time/residue: 0.1957 time to fit residues: 38.4995 Evaluate side-chains 160 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 0.0050 chunk 37 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5154 Z= 0.186 Angle : 0.622 7.847 7001 Z= 0.324 Chirality : 0.046 0.185 763 Planarity : 0.004 0.053 891 Dihedral : 5.455 73.757 754 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.89 % Allowed : 21.56 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.36 (0.32), residues: 638 helix: -3.47 (0.67), residues: 33 sheet: -0.94 (0.34), residues: 224 loop : -1.82 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.002 0.001 HIS C 99 PHE 0.015 0.002 PHE C 68 TYR 0.018 0.002 TYR E 94 ARG 0.009 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 GLU cc_start: 0.6131 (mp0) cc_final: 0.5923 (mp0) REVERT: C 34 MET cc_start: 0.8168 (ptp) cc_final: 0.7924 (ptp) REVERT: C 43 LYS cc_start: 0.8706 (mmtm) cc_final: 0.8470 (mmmt) REVERT: C 73 ASP cc_start: 0.7010 (t70) cc_final: 0.6251 (t70) REVERT: C 89 GLU cc_start: 0.7762 (mp0) cc_final: 0.7187 (mp0) REVERT: C 103 GLN cc_start: 0.8611 (mp10) cc_final: 0.8069 (mp10) REVERT: E 24 ARG cc_start: 0.7563 (ttp-110) cc_final: 0.6782 (ttm110) REVERT: E 27 GLN cc_start: 0.8455 (tt0) cc_final: 0.8016 (mp10) REVERT: E 82 ASP cc_start: 0.8608 (m-30) cc_final: 0.8211 (m-30) REVERT: E 89 GLN cc_start: 0.8139 (tm130) cc_final: 0.7310 (tm-30) REVERT: G 340 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8298 (mp0) REVERT: G 353 TRP cc_start: 0.8015 (p-90) cc_final: 0.7506 (p-90) REVERT: G 369 TYR cc_start: 0.9069 (t80) cc_final: 0.8474 (t80) REVERT: G 465 GLU cc_start: 0.8445 (tt0) cc_final: 0.8165 (tt0) REVERT: G 471 GLU cc_start: 0.7983 (tt0) cc_final: 0.7496 (pt0) REVERT: L 44 LYS cc_start: 0.7029 (mtmm) cc_final: 0.6717 (ttpt) REVERT: H 73 ASP cc_start: 0.7202 (t0) cc_final: 0.6012 (t0) REVERT: H 76 MET cc_start: 0.8072 (mpp) cc_final: 0.7440 (mpp) REVERT: H 78 THR cc_start: 0.6108 (OUTLIER) cc_final: 0.5517 (t) outliers start: 27 outliers final: 22 residues processed: 155 average time/residue: 0.1881 time to fit residues: 36.5453 Evaluate side-chains 157 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5154 Z= 0.286 Angle : 0.696 9.590 7001 Z= 0.361 Chirality : 0.047 0.191 763 Planarity : 0.005 0.054 891 Dihedral : 5.740 76.879 754 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 5.62 % Allowed : 21.38 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 (0.31), residues: 638 helix: -3.61 (0.64), residues: 33 sheet: -0.93 (0.35), residues: 214 loop : -1.93 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 106 HIS 0.003 0.001 HIS L 88 PHE 0.018 0.002 PHE G 347 TYR 0.021 0.002 TYR C 95 ARG 0.009 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 GLU cc_start: 0.6132 (mp0) cc_final: 0.5896 (mp0) REVERT: C 43 LYS cc_start: 0.8702 (mmtm) cc_final: 0.8471 (mmmt) REVERT: C 73 ASP cc_start: 0.7159 (t70) cc_final: 0.6350 (t70) REVERT: C 81 LEU cc_start: 0.6126 (tt) cc_final: 0.5857 (tt) REVERT: C 89 GLU cc_start: 0.7772 (mp0) cc_final: 0.7176 (mp0) REVERT: E 24 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.6581 (ttm170) REVERT: E 27 GLN cc_start: 0.8445 (tt0) cc_final: 0.7950 (mt0) REVERT: E 82 ASP cc_start: 0.8577 (m-30) cc_final: 0.8148 (m-30) REVERT: E 90 GLN cc_start: 0.7667 (pp30) cc_final: 0.7236 (pp30) REVERT: G 340 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8319 (mp0) REVERT: G 353 TRP cc_start: 0.8069 (p-90) cc_final: 0.7601 (p-90) REVERT: G 369 TYR cc_start: 0.9071 (t80) cc_final: 0.8515 (t80) REVERT: G 457 ARG cc_start: 0.8273 (ttt-90) cc_final: 0.7758 (ttt-90) REVERT: G 465 GLU cc_start: 0.8494 (tt0) cc_final: 0.8275 (tt0) REVERT: G 471 GLU cc_start: 0.8003 (tt0) cc_final: 0.7486 (pt0) REVERT: L 44 LYS cc_start: 0.7011 (mtmm) cc_final: 0.6694 (pttt) REVERT: H 73 ASP cc_start: 0.7273 (t0) cc_final: 0.6673 (t0) REVERT: H 90 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7359 (t0) outliers start: 31 outliers final: 26 residues processed: 155 average time/residue: 0.2185 time to fit residues: 42.2500 Evaluate side-chains 162 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 51 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5154 Z= 0.180 Angle : 0.636 9.245 7001 Z= 0.327 Chirality : 0.045 0.163 763 Planarity : 0.004 0.053 891 Dihedral : 5.553 75.334 754 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.07 % Allowed : 21.92 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.35 (0.32), residues: 638 helix: -3.38 (0.72), residues: 33 sheet: -0.97 (0.35), residues: 220 loop : -1.79 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 106 HIS 0.003 0.001 HIS C 99 PHE 0.013 0.001 PHE G 377 TYR 0.018 0.002 TYR E 94 ARG 0.010 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.8698 (mmtm) cc_final: 0.8466 (mmmt) REVERT: C 73 ASP cc_start: 0.7025 (t70) cc_final: 0.6264 (t70) REVERT: C 89 GLU cc_start: 0.7796 (mp0) cc_final: 0.7194 (mp0) REVERT: E 24 ARG cc_start: 0.7572 (ttp-110) cc_final: 0.7144 (ttm110) REVERT: E 27 GLN cc_start: 0.8455 (tt0) cc_final: 0.7958 (mt0) REVERT: E 82 ASP cc_start: 0.8594 (m-30) cc_final: 0.8184 (m-30) REVERT: E 89 GLN cc_start: 0.8190 (tm130) cc_final: 0.7495 (tm-30) REVERT: E 90 GLN cc_start: 0.7942 (pp30) cc_final: 0.7414 (pp30) REVERT: G 340 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8306 (mp0) REVERT: G 353 TRP cc_start: 0.8088 (p-90) cc_final: 0.7586 (p-90) REVERT: G 369 TYR cc_start: 0.9082 (t80) cc_final: 0.8502 (t80) REVERT: G 457 ARG cc_start: 0.8221 (ttt-90) cc_final: 0.7818 (ttt-90) REVERT: G 462 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7529 (mtmm) REVERT: G 465 GLU cc_start: 0.8432 (tt0) cc_final: 0.7998 (tt0) REVERT: G 471 GLU cc_start: 0.7988 (tt0) cc_final: 0.7477 (pt0) REVERT: L 28 SER cc_start: 0.9309 (t) cc_final: 0.9072 (p) REVERT: L 100 LYS cc_start: 0.8425 (tmtt) cc_final: 0.8059 (tmtt) REVERT: H 73 ASP cc_start: 0.7231 (t0) cc_final: 0.6509 (t0) REVERT: H 78 THR cc_start: 0.5783 (OUTLIER) cc_final: 0.5213 (t) outliers start: 28 outliers final: 26 residues processed: 152 average time/residue: 0.1773 time to fit residues: 34.2184 Evaluate side-chains 161 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 4.9990 chunk 57 optimal weight: 0.0770 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5154 Z= 0.200 Angle : 0.677 10.139 7001 Z= 0.346 Chirality : 0.046 0.157 763 Planarity : 0.004 0.054 891 Dihedral : 5.511 74.765 754 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.89 % Allowed : 22.83 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.24 (0.32), residues: 638 helix: -3.20 (0.77), residues: 33 sheet: -0.91 (0.35), residues: 217 loop : -1.71 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.002 0.001 HIS C 99 PHE 0.013 0.001 PHE G 377 TYR 0.018 0.001 TYR E 94 ARG 0.011 0.001 ARG E 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.8698 (mmtm) cc_final: 0.8467 (mmmt) REVERT: C 73 ASP cc_start: 0.7032 (t70) cc_final: 0.6225 (t0) REVERT: C 89 GLU cc_start: 0.7812 (mp0) cc_final: 0.7220 (mp0) REVERT: E 24 ARG cc_start: 0.7555 (ttp-110) cc_final: 0.7128 (ttm110) REVERT: E 27 GLN cc_start: 0.8430 (tt0) cc_final: 0.7941 (mt0) REVERT: E 79 GLN cc_start: 0.8322 (mm110) cc_final: 0.7646 (mm110) REVERT: E 82 ASP cc_start: 0.8470 (m-30) cc_final: 0.7858 (m-30) REVERT: E 89 GLN cc_start: 0.7880 (tm130) cc_final: 0.7396 (tm-30) REVERT: E 90 GLN cc_start: 0.7899 (pp30) cc_final: 0.7690 (pp30) REVERT: G 340 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8308 (mp0) REVERT: G 353 TRP cc_start: 0.8057 (p-90) cc_final: 0.7561 (p-90) REVERT: G 369 TYR cc_start: 0.9082 (t80) cc_final: 0.8542 (t80) REVERT: G 457 ARG cc_start: 0.8210 (ttt-90) cc_final: 0.7610 (ttt-90) REVERT: G 462 LYS cc_start: 0.7842 (mtmm) cc_final: 0.7525 (mtmm) REVERT: G 465 GLU cc_start: 0.8438 (tt0) cc_final: 0.8073 (tt0) REVERT: G 471 GLU cc_start: 0.7993 (tt0) cc_final: 0.7500 (pt0) REVERT: L 28 SER cc_start: 0.9311 (t) cc_final: 0.9061 (p) REVERT: H 73 ASP cc_start: 0.7219 (t0) cc_final: 0.6486 (t0) REVERT: H 78 THR cc_start: 0.5721 (OUTLIER) cc_final: 0.5136 (t) outliers start: 27 outliers final: 25 residues processed: 153 average time/residue: 0.1767 time to fit residues: 34.4351 Evaluate side-chains 156 residues out of total 552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 388 ASN ** 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 = 0.3417 r_free = 0.3417 target = 0.112937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.095604 restraints weight = 10279.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098726 restraints weight = 5857.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100875 restraints weight = 3984.169| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5154 Z= 0.238 Angle : 0.693 9.973 7001 Z= 0.356 Chirality : 0.046 0.153 763 Planarity : 0.004 0.054 891 Dihedral : 5.645 75.860 754 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 5.25 % Allowed : 23.91 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.25 (0.32), residues: 638 helix: -3.11 (0.77), residues: 33 sheet: -0.95 (0.35), residues: 217 loop : -1.70 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 106 HIS 0.002 0.001 HIS L 88 PHE 0.015 0.002 PHE G 347 TYR 0.019 0.002 TYR E 94 ARG 0.005 0.001 ARG G 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2190.59 seconds wall clock time: 40 minutes 46.23 seconds (2446.23 seconds total)