Starting phenix.real_space_refine on Sun Mar 10 21:05:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv4_35740/03_2024/8iv4_35740.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv4_35740/03_2024/8iv4_35740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv4_35740/03_2024/8iv4_35740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv4_35740/03_2024/8iv4_35740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv4_35740/03_2024/8iv4_35740.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv4_35740/03_2024/8iv4_35740.pdb" } resolution = 3.59 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 3173 2.51 5 N 841 2.21 5 O 980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 31": "OD1" <-> "OD2" Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1": "OD1" <-> "OD2" Residue "B PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 60": "OD1" <-> "OD2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 5": "OE1" <-> "OE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 357": "NH1" <-> "NH2" Residue "G PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 408": "NH1" <-> "NH2" Residue "G TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 484": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5027 Number of models: 1 Model: "" Number of chains: 6 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: "B" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 921 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} 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: "C" 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: 3.30, per 1000 atoms: 0.66 Number of scatterers: 5027 At special positions: 0 Unit cell: (86.358, 66.908, 109.698, 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 33 16.00 O 980 8.00 N 841 7.00 C 3173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 98 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " 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 C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN G 343 " Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 921.0 milliseconds 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 12 sheets defined 6.2% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.002A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.801A pdb=" N ASP B 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 83 " --> pdb=" O CYS B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.918A pdb=" N TRP G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 370 removed outlier: 3.923A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.482A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE G 410 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 removed outlier: 3.698A pdb=" N TYR G 421 " --> pdb=" O LYS G 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.745A pdb=" N SER L 7 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR L 68 " --> pdb=" O VAL L 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.532A pdb=" N GLU L 102 " --> pdb=" O MET L 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.560A pdb=" N TYR L 48 " --> pdb=" O ASN L 52 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN L 36 " --> pdb=" O VAL L 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.521A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.535A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR H 94 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.535A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR H 94 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.565A pdb=" N GLU B 105 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP B 35 " --> pdb=" O MET B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.519A pdb=" N GLY A 10 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET A 34 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'G' and resid 452 through 454 146 hydrogen bonds defined for protein. 357 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: 1.39 Time building geometry restraints manager: 1.88 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: 1593 1.34 - 1.46: 1294 1.46 - 1.58: 2212 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 5147 Sorted by residual: bond pdb=" C LEU G 335 " pdb=" N CYS G 336 " ideal model delta sigma weight residual 1.331 1.269 0.062 2.07e-02 2.33e+03 8.86e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" N TYR G 473 " pdb=" CA TYR G 473 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.31e+00 bond pdb=" N CYS G 488 " pdb=" CA CYS G 488 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.10e+00 ... (remaining 5142 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.94: 138 106.94 - 113.79: 2749 113.79 - 120.64: 2019 120.64 - 127.49: 2017 127.49 - 134.34: 52 Bond angle restraints: 6975 Sorted by residual: angle pdb=" C SER L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 angle pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N TYR B 94 " pdb=" CA TYR B 94 " pdb=" C TYR B 94 " ideal model delta sigma weight residual 109.81 118.28 -8.47 2.21e+00 2.05e-01 1.47e+01 angle pdb=" C GLN L 89 " pdb=" N TRP L 90 " pdb=" CA TRP L 90 " ideal model delta sigma weight residual 120.63 126.24 -5.61 1.61e+00 3.86e-01 1.21e+01 angle pdb=" N GLN A 111 " pdb=" CA GLN A 111 " pdb=" C GLN A 111 " ideal model delta sigma weight residual 114.56 110.26 4.30 1.27e+00 6.20e-01 1.14e+01 ... (remaining 6970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 2744 17.91 - 35.81: 253 35.81 - 53.72: 45 53.72 - 71.62: 4 71.62 - 89.53: 5 Dihedral angle restraints: 3051 sinusoidal: 1201 harmonic: 1850 Sorted by residual: dihedral pdb=" CA ASN G 487 " pdb=" C ASN G 487 " pdb=" N CYS G 488 " pdb=" CA CYS G 488 " ideal model delta harmonic sigma weight residual -180.00 -131.59 -48.41 0 5.00e+00 4.00e-02 9.38e+01 dihedral pdb=" CA CYS G 361 " pdb=" C CYS G 361 " pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 58.47 34.53 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 3048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 514 0.047 - 0.094: 171 0.094 - 0.141: 56 0.141 - 0.188: 9 0.188 - 0.235: 4 Chirality restraints: 754 Sorted by residual: chirality pdb=" CB VAL H 48 " pdb=" CA VAL H 48 " pdb=" CG1 VAL H 48 " pdb=" CG2 VAL H 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR A 28 " pdb=" CA THR A 28 " pdb=" OG1 THR A 28 " pdb=" CG2 THR A 28 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA TYR B 94 " pdb=" N TYR B 94 " pdb=" C TYR B 94 " pdb=" CB TYR B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 751 not shown) Planarity restraints: 892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 487 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ASN G 487 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN G 487 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS G 488 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 94 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO B 95 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 520 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO G 521 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 521 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 521 " 0.035 5.00e-02 4.00e+02 ... (remaining 889 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1626 2.83 - 3.35: 3861 3.35 - 3.87: 8003 3.87 - 4.38: 8760 4.38 - 4.90: 16095 Nonbonded interactions: 38345 Sorted by model distance: nonbonded pdb=" O SER G 438 " pdb=" OG SER G 438 " model vdw 2.315 2.440 nonbonded pdb=" O SER H 30 " pdb=" OG SER H 30 " model vdw 2.327 2.440 nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.336 2.440 nonbonded pdb=" O ARG H 67 " pdb=" OG SER H 84 " model vdw 2.354 2.440 nonbonded pdb=" OG SER G 438 " pdb=" OD2 ASP G 442 " model vdw 2.361 2.440 ... (remaining 38340 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=0.83 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: 12.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 38.380 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.450 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 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 : 0.005 0.062 5147 Z= 0.355 Angle : 0.842 8.466 6975 Z= 0.493 Chirality : 0.054 0.235 754 Planarity : 0.007 0.069 891 Dihedral : 14.005 89.529 1855 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.55 % Allowed : 6.96 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.27), residues: 634 helix: -4.95 (0.21), residues: 21 sheet: -1.94 (0.31), residues: 250 loop : -3.14 (0.24), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 47 HIS 0.004 0.001 HIS B 91 PHE 0.022 0.002 PHE L 46 TYR 0.026 0.002 TYR B 94 ARG 0.001 0.000 ARG G 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 0.561 Fit side-chains REVERT: L 11 MET cc_start: 0.7400 (mtt) cc_final: 0.6839 (mtt) REVERT: L 19 ILE cc_start: 0.8245 (tt) cc_final: 0.8027 (tt) REVERT: L 32 MET cc_start: 0.7935 (tpp) cc_final: 0.7538 (tpp) REVERT: L 90 TRP cc_start: 0.7295 (t60) cc_final: 0.7030 (t60) REVERT: H 3 MET cc_start: 0.6729 (mtm) cc_final: 0.5999 (tpt) REVERT: H 19 LYS cc_start: 0.7516 (tttt) cc_final: 0.7029 (tttm) REVERT: H 82 GLN cc_start: 0.7352 (pp30) cc_final: 0.7110 (pp30) REVERT: H 93 MET cc_start: 0.6589 (ttm) cc_final: 0.6235 (ttm) REVERT: H 109 ASP cc_start: 0.8068 (m-30) cc_final: 0.7447 (m-30) REVERT: B 1 ASP cc_start: 0.7827 (p0) cc_final: 0.7625 (p0) REVERT: B 4 MET cc_start: 0.6457 (mmm) cc_final: 0.5943 (mmt) REVERT: B 47 MET cc_start: 0.7245 (mmp) cc_final: 0.6926 (mmp) REVERT: B 52 SER cc_start: 0.8365 (t) cc_final: 0.8140 (m) REVERT: B 54 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7763 (ttp80) REVERT: B 79 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7432 (mm110) REVERT: B 82 ASP cc_start: 0.8596 (m-30) cc_final: 0.8362 (m-30) REVERT: A 18 MET cc_start: 0.6312 (ttm) cc_final: 0.6019 (ttt) REVERT: A 19 LYS cc_start: 0.7633 (tttt) cc_final: 0.6874 (tttp) REVERT: A 35 ASP cc_start: 0.6952 (m-30) cc_final: 0.6541 (m-30) REVERT: A 50 GLN cc_start: 0.7547 (tt0) cc_final: 0.6930 (tt0) REVERT: A 69 ARG cc_start: 0.7395 (mtm110) cc_final: 0.7149 (mtp180) REVERT: A 108 PHE cc_start: 0.7478 (t80) cc_final: 0.7176 (t80) REVERT: G 347 PHE cc_start: 0.8147 (m-10) cc_final: 0.7861 (m-80) REVERT: G 369 TYR cc_start: 0.8841 (t80) cc_final: 0.8477 (t80) REVERT: G 442 ASP cc_start: 0.8779 (m-30) cc_final: 0.8098 (m-30) outliers start: 3 outliers final: 1 residues processed: 128 average time/residue: 0.1972 time to fit residues: 31.1394 Evaluate side-chains 103 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 36 GLN B 79 GLN A 13 GLN G 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5147 Z= 0.234 Angle : 0.574 6.716 6975 Z= 0.306 Chirality : 0.044 0.152 754 Planarity : 0.005 0.059 891 Dihedral : 6.279 69.499 752 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.41 % Favored : 92.43 % Rotamer: Outliers : 3.66 % Allowed : 10.81 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.30 (0.29), residues: 634 helix: -4.26 (0.50), residues: 15 sheet: -1.54 (0.30), residues: 257 loop : -2.67 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 90 HIS 0.002 0.001 HIS L 88 PHE 0.015 0.001 PHE L 46 TYR 0.017 0.001 TYR B 94 ARG 0.004 0.000 ARG G 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 MET cc_start: 0.7267 (mtt) cc_final: 0.6864 (mtt) REVERT: L 18 GLU cc_start: 0.8273 (pp20) cc_final: 0.7617 (pp20) REVERT: L 90 TRP cc_start: 0.7338 (t60) cc_final: 0.6824 (t60) REVERT: H 3 MET cc_start: 0.6140 (mtm) cc_final: 0.5512 (tpt) REVERT: H 19 LYS cc_start: 0.7540 (tttt) cc_final: 0.6906 (tttm) REVERT: H 82 GLN cc_start: 0.6845 (pp30) cc_final: 0.6469 (tm-30) REVERT: H 109 ASP cc_start: 0.7974 (m-30) cc_final: 0.7307 (m-30) REVERT: B 1 ASP cc_start: 0.7941 (p0) cc_final: 0.7710 (p0) REVERT: B 30 ARG cc_start: 0.7106 (mpt90) cc_final: 0.6674 (mmt-90) REVERT: B 42 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7597 (mt0) REVERT: B 47 MET cc_start: 0.7269 (mmp) cc_final: 0.6928 (mmp) REVERT: B 54 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7555 (ttp80) REVERT: B 89 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6833 (pt) REVERT: A 19 LYS cc_start: 0.7310 (tttt) cc_final: 0.6648 (tttp) REVERT: A 108 PHE cc_start: 0.7513 (t80) cc_final: 0.7209 (t80) outliers start: 20 outliers final: 13 residues processed: 119 average time/residue: 0.2071 time to fit residues: 30.3130 Evaluate side-chains 116 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN B 55 HIS A 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5147 Z= 0.296 Angle : 0.584 9.137 6975 Z= 0.307 Chirality : 0.045 0.161 754 Planarity : 0.005 0.056 891 Dihedral : 6.038 60.096 752 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 6.59 % Allowed : 12.45 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.76 (0.30), residues: 634 helix: -3.59 (0.76), residues: 15 sheet: -1.25 (0.31), residues: 254 loop : -2.25 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 90 HIS 0.003 0.001 HIS L 88 PHE 0.011 0.001 PHE L 46 TYR 0.018 0.002 TYR B 94 ARG 0.004 0.000 ARG G 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: L 11 MET cc_start: 0.7546 (mtt) cc_final: 0.7285 (mtt) REVERT: L 18 GLU cc_start: 0.8282 (pp20) cc_final: 0.7672 (pp20) REVERT: H 3 MET cc_start: 0.6093 (mtm) cc_final: 0.5493 (tpt) REVERT: H 19 LYS cc_start: 0.7534 (tttt) cc_final: 0.6914 (tttm) REVERT: H 82 GLN cc_start: 0.6642 (pp30) cc_final: 0.6303 (tm-30) REVERT: H 109 ASP cc_start: 0.7896 (m-30) cc_final: 0.7115 (m-30) REVERT: B 30 ARG cc_start: 0.7217 (mpt90) cc_final: 0.6864 (mmt-90) REVERT: B 42 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7598 (mt0) REVERT: B 47 MET cc_start: 0.7120 (mmp) cc_final: 0.6824 (mmp) REVERT: B 54 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7665 (ttp80) REVERT: B 89 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7027 (pt) REVERT: A 18 MET cc_start: 0.6246 (ttt) cc_final: 0.5960 (ttt) REVERT: A 19 LYS cc_start: 0.7434 (tttt) cc_final: 0.6802 (ttmm) REVERT: G 369 TYR cc_start: 0.8802 (t80) cc_final: 0.8442 (t80) REVERT: G 503 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7766 (t) outliers start: 36 outliers final: 27 residues processed: 125 average time/residue: 0.1916 time to fit residues: 29.8536 Evaluate side-chains 132 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5147 Z= 0.240 Angle : 0.552 7.123 6975 Z= 0.292 Chirality : 0.044 0.164 754 Planarity : 0.004 0.055 891 Dihedral : 5.847 51.853 752 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 6.23 % Allowed : 14.65 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.31), residues: 634 helix: -2.98 (1.03), residues: 15 sheet: -0.90 (0.31), residues: 246 loop : -2.07 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 33 HIS 0.003 0.001 HIS L 88 PHE 0.009 0.001 PHE A 70 TYR 0.026 0.002 TYR H 32 ARG 0.006 0.000 ARG G 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: L 11 MET cc_start: 0.7608 (mtt) cc_final: 0.7349 (mtt) REVERT: L 18 GLU cc_start: 0.8284 (pp20) cc_final: 0.7694 (pp20) REVERT: L 90 TRP cc_start: 0.7590 (t60) cc_final: 0.7118 (t60) REVERT: H 3 MET cc_start: 0.6090 (mtm) cc_final: 0.5506 (tpt) REVERT: H 19 LYS cc_start: 0.7504 (tttt) cc_final: 0.6919 (tttm) REVERT: H 109 ASP cc_start: 0.7940 (m-30) cc_final: 0.7190 (m-30) REVERT: B 30 ARG cc_start: 0.7149 (mpt90) cc_final: 0.6830 (mmt-90) REVERT: B 42 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7590 (mt0) REVERT: B 47 MET cc_start: 0.7044 (mmp) cc_final: 0.6695 (mmp) REVERT: B 54 ARG cc_start: 0.8084 (ttm110) cc_final: 0.7641 (ttp80) REVERT: B 89 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6966 (pt) REVERT: A 18 MET cc_start: 0.6261 (ttt) cc_final: 0.5896 (ttt) REVERT: A 19 LYS cc_start: 0.7458 (tttt) cc_final: 0.6809 (tttp) REVERT: G 369 TYR cc_start: 0.8778 (t80) cc_final: 0.8427 (t80) REVERT: G 503 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7703 (t) outliers start: 34 outliers final: 28 residues processed: 125 average time/residue: 0.2056 time to fit residues: 32.2978 Evaluate side-chains 135 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5147 Z= 0.240 Angle : 0.548 6.675 6975 Z= 0.290 Chirality : 0.044 0.165 754 Planarity : 0.005 0.087 891 Dihedral : 5.885 47.982 752 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 7.33 % Allowed : 14.47 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.23 (0.32), residues: 634 helix: -2.56 (1.18), residues: 15 sheet: -0.76 (0.32), residues: 245 loop : -1.99 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 33 HIS 0.006 0.001 HIS B 55 PHE 0.009 0.001 PHE A 70 TYR 0.032 0.002 TYR H 32 ARG 0.010 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 106 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: L 11 MET cc_start: 0.7602 (mtt) cc_final: 0.7347 (mtt) REVERT: L 18 GLU cc_start: 0.8255 (pp20) cc_final: 0.7666 (pp20) REVERT: L 32 MET cc_start: 0.7226 (tpp) cc_final: 0.6971 (tpp) REVERT: L 90 TRP cc_start: 0.7578 (t60) cc_final: 0.6896 (t60) REVERT: H 3 MET cc_start: 0.6031 (mtm) cc_final: 0.5438 (tpt) REVERT: H 19 LYS cc_start: 0.7506 (tttt) cc_final: 0.6918 (tttm) REVERT: H 28 SER cc_start: 0.7973 (t) cc_final: 0.7639 (p) REVERT: H 108 MET cc_start: 0.7852 (mtt) cc_final: 0.7607 (mtp) REVERT: H 109 ASP cc_start: 0.8029 (m-30) cc_final: 0.7231 (m-30) REVERT: H 110 TYR cc_start: 0.6954 (m-80) cc_final: 0.6629 (m-80) REVERT: B 30 ARG cc_start: 0.7161 (mpt90) cc_final: 0.6895 (mmt-90) REVERT: B 42 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7671 (mt0) REVERT: B 47 MET cc_start: 0.6961 (mmp) cc_final: 0.6621 (mmp) REVERT: B 54 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7672 (ttp80) REVERT: B 89 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6950 (pt) REVERT: A 18 MET cc_start: 0.6240 (ttt) cc_final: 0.5989 (ttt) REVERT: A 19 LYS cc_start: 0.7452 (tttt) cc_final: 0.6816 (tttp) REVERT: A 25 SER cc_start: 0.6292 (m) cc_final: 0.5899 (p) REVERT: G 369 TYR cc_start: 0.8761 (t80) cc_final: 0.8385 (t80) REVERT: G 503 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7673 (t) outliers start: 40 outliers final: 31 residues processed: 126 average time/residue: 0.1817 time to fit residues: 29.1629 Evaluate side-chains 137 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 0.0000 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS G 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5147 Z= 0.284 Angle : 0.567 7.141 6975 Z= 0.301 Chirality : 0.045 0.181 754 Planarity : 0.005 0.078 891 Dihedral : 5.927 45.362 752 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 7.14 % Allowed : 15.38 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.17 (0.32), residues: 634 helix: -2.45 (1.22), residues: 15 sheet: -0.71 (0.32), residues: 245 loop : -1.97 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 90 HIS 0.012 0.002 HIS B 55 PHE 0.009 0.001 PHE A 70 TYR 0.025 0.002 TYR H 32 ARG 0.008 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 108 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: L 11 MET cc_start: 0.7591 (mtt) cc_final: 0.7320 (mtt) REVERT: L 18 GLU cc_start: 0.8209 (pp20) cc_final: 0.7641 (pp20) REVERT: L 90 TRP cc_start: 0.7619 (t60) cc_final: 0.6990 (t60) REVERT: H 3 MET cc_start: 0.5969 (mtm) cc_final: 0.5376 (tpt) REVERT: H 19 LYS cc_start: 0.7464 (tttt) cc_final: 0.6958 (tttm) REVERT: H 28 SER cc_start: 0.7956 (t) cc_final: 0.7717 (p) REVERT: H 82 GLN cc_start: 0.6708 (tm-30) cc_final: 0.6372 (tt0) REVERT: H 108 MET cc_start: 0.7869 (mtt) cc_final: 0.7627 (mtp) REVERT: H 109 ASP cc_start: 0.8020 (m-30) cc_final: 0.7269 (m-30) REVERT: B 4 MET cc_start: 0.6675 (mmm) cc_final: 0.5549 (mmm) REVERT: B 30 ARG cc_start: 0.7150 (mpt90) cc_final: 0.6894 (mmt-90) REVERT: B 42 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7693 (mt0) REVERT: B 47 MET cc_start: 0.6886 (mmp) cc_final: 0.6615 (mmp) REVERT: B 54 ARG cc_start: 0.8071 (ttm110) cc_final: 0.7626 (ttp80) REVERT: B 89 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6928 (pt) REVERT: A 18 MET cc_start: 0.6180 (ttt) cc_final: 0.5846 (ttt) REVERT: A 19 LYS cc_start: 0.7489 (tttt) cc_final: 0.6864 (tttp) REVERT: A 25 SER cc_start: 0.6336 (m) cc_final: 0.5925 (p) REVERT: G 369 TYR cc_start: 0.8757 (t80) cc_final: 0.8416 (t80) REVERT: G 503 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7687 (t) outliers start: 39 outliers final: 30 residues processed: 128 average time/residue: 0.1714 time to fit residues: 28.0200 Evaluate side-chains 133 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS G 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5147 Z= 0.286 Angle : 0.599 8.713 6975 Z= 0.312 Chirality : 0.046 0.205 754 Planarity : 0.005 0.072 891 Dihedral : 5.820 43.000 752 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 7.33 % Allowed : 16.48 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.13 (0.32), residues: 634 helix: -2.38 (1.26), residues: 15 sheet: -0.72 (0.32), residues: 247 loop : -1.92 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 90 HIS 0.004 0.001 HIS L 88 PHE 0.009 0.001 PHE A 70 TYR 0.022 0.002 TYR H 32 ARG 0.007 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 105 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 MET cc_start: 0.7604 (mtt) cc_final: 0.7366 (mtt) REVERT: L 32 MET cc_start: 0.7138 (tpp) cc_final: 0.6900 (mtp) REVERT: H 3 MET cc_start: 0.5944 (mtm) cc_final: 0.5369 (tpt) REVERT: H 19 LYS cc_start: 0.7462 (tttt) cc_final: 0.6960 (tttm) REVERT: H 28 SER cc_start: 0.7945 (t) cc_final: 0.7743 (p) REVERT: H 82 GLN cc_start: 0.6658 (tm-30) cc_final: 0.6413 (tt0) REVERT: H 108 MET cc_start: 0.7888 (mtt) cc_final: 0.7661 (mtp) REVERT: H 109 ASP cc_start: 0.8035 (m-30) cc_final: 0.7293 (m-30) REVERT: B 4 MET cc_start: 0.6712 (mmm) cc_final: 0.5673 (mmm) REVERT: B 30 ARG cc_start: 0.7157 (mpt90) cc_final: 0.6909 (mmt-90) REVERT: B 42 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7705 (mt0) REVERT: B 47 MET cc_start: 0.6990 (mmp) cc_final: 0.6636 (mmp) REVERT: B 54 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7654 (ttp80) REVERT: A 18 MET cc_start: 0.6151 (ttt) cc_final: 0.5932 (ttt) REVERT: A 19 LYS cc_start: 0.7443 (tttt) cc_final: 0.6843 (tttp) REVERT: A 25 SER cc_start: 0.6325 (m) cc_final: 0.5919 (p) REVERT: G 465 GLU cc_start: 0.7439 (tt0) cc_final: 0.7121 (tt0) REVERT: G 503 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.7814 (t) outliers start: 40 outliers final: 33 residues processed: 125 average time/residue: 0.1777 time to fit residues: 28.2895 Evaluate side-chains 138 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 104 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5147 Z= 0.306 Angle : 0.616 9.358 6975 Z= 0.319 Chirality : 0.046 0.228 754 Planarity : 0.005 0.072 891 Dihedral : 5.802 42.677 752 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 6.96 % Allowed : 18.50 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.08 (0.32), residues: 634 helix: -2.11 (1.28), residues: 15 sheet: -0.75 (0.32), residues: 249 loop : -1.85 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 436 HIS 0.005 0.001 HIS B 55 PHE 0.008 0.001 PHE G 429 TYR 0.031 0.002 TYR A 61 ARG 0.007 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 106 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 MET cc_start: 0.7635 (mtt) cc_final: 0.7423 (mtt) REVERT: L 32 MET cc_start: 0.7201 (tpp) cc_final: 0.6946 (mtp) REVERT: L 46 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.6725 (t80) REVERT: H 3 MET cc_start: 0.5963 (mtm) cc_final: 0.5388 (tpt) REVERT: H 19 LYS cc_start: 0.7539 (tttt) cc_final: 0.7033 (tttm) REVERT: H 28 SER cc_start: 0.7989 (t) cc_final: 0.7780 (p) REVERT: H 82 GLN cc_start: 0.6814 (tm-30) cc_final: 0.6530 (tt0) REVERT: H 108 MET cc_start: 0.7884 (mtt) cc_final: 0.7658 (mtp) REVERT: H 109 ASP cc_start: 0.8012 (m-30) cc_final: 0.7261 (m-30) REVERT: B 4 MET cc_start: 0.6699 (mmm) cc_final: 0.5675 (mmm) REVERT: B 30 ARG cc_start: 0.7141 (mpt90) cc_final: 0.6904 (mmt-90) REVERT: B 42 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7734 (mt0) REVERT: B 47 MET cc_start: 0.6915 (mmp) cc_final: 0.6557 (mmp) REVERT: B 54 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7708 (ttp80) REVERT: A 18 MET cc_start: 0.6377 (ttt) cc_final: 0.6019 (ttt) REVERT: A 19 LYS cc_start: 0.7553 (tttt) cc_final: 0.6914 (tttp) REVERT: A 25 SER cc_start: 0.6334 (m) cc_final: 0.5931 (p) REVERT: G 465 GLU cc_start: 0.7415 (tt0) cc_final: 0.7098 (tt0) outliers start: 38 outliers final: 34 residues processed: 125 average time/residue: 0.1857 time to fit residues: 29.4749 Evaluate side-chains 140 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 105 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 478 THR Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5147 Z= 0.202 Angle : 0.574 8.095 6975 Z= 0.297 Chirality : 0.045 0.209 754 Planarity : 0.005 0.073 891 Dihedral : 5.535 41.596 752 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 5.86 % Allowed : 19.23 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.32), residues: 634 helix: -1.87 (1.33), residues: 15 sheet: -0.71 (0.32), residues: 248 loop : -1.72 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 93 HIS 0.003 0.001 HIS L 88 PHE 0.007 0.001 PHE B 62 TYR 0.023 0.002 TYR A 61 ARG 0.007 0.000 ARG G 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 MET cc_start: 0.7708 (mtt) cc_final: 0.7472 (mtt) REVERT: L 46 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.6658 (t80) REVERT: H 3 MET cc_start: 0.5926 (mtm) cc_final: 0.5351 (tpt) REVERT: H 19 LYS cc_start: 0.7528 (tttt) cc_final: 0.7059 (tttm) REVERT: H 28 SER cc_start: 0.7976 (t) cc_final: 0.7760 (p) REVERT: H 73 ASP cc_start: 0.6622 (m-30) cc_final: 0.6208 (m-30) REVERT: H 108 MET cc_start: 0.7885 (mtt) cc_final: 0.7683 (mtp) REVERT: H 109 ASP cc_start: 0.8069 (m-30) cc_final: 0.7324 (m-30) REVERT: B 4 MET cc_start: 0.6709 (mmm) cc_final: 0.5714 (mmm) REVERT: B 30 ARG cc_start: 0.7116 (mpt90) cc_final: 0.6881 (mmt-90) REVERT: B 42 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7767 (mt0) REVERT: B 47 MET cc_start: 0.6976 (mmp) cc_final: 0.6648 (mmp) REVERT: B 54 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7717 (ttp80) REVERT: A 18 MET cc_start: 0.6431 (ttt) cc_final: 0.6003 (ttt) REVERT: A 19 LYS cc_start: 0.7406 (tttt) cc_final: 0.6778 (tttp) REVERT: A 25 SER cc_start: 0.6251 (m) cc_final: 0.5857 (p) REVERT: G 465 GLU cc_start: 0.7453 (tt0) cc_final: 0.7133 (tt0) outliers start: 32 outliers final: 28 residues processed: 125 average time/residue: 0.1778 time to fit residues: 28.2391 Evaluate side-chains 136 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 478 THR Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5147 Z= 0.195 Angle : 0.572 7.969 6975 Z= 0.296 Chirality : 0.044 0.201 754 Planarity : 0.005 0.068 891 Dihedral : 5.385 41.550 752 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 5.31 % Allowed : 19.96 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.87 (0.33), residues: 634 helix: -1.79 (1.35), residues: 15 sheet: -0.57 (0.33), residues: 243 loop : -1.72 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 93 HIS 0.005 0.001 HIS L 88 PHE 0.007 0.001 PHE B 62 TYR 0.021 0.001 TYR A 61 ARG 0.007 0.000 ARG G 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 11 MET cc_start: 0.7718 (mtt) cc_final: 0.7491 (mtt) REVERT: L 46 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.6743 (t80) REVERT: H 3 MET cc_start: 0.5972 (mtm) cc_final: 0.5384 (tpt) REVERT: H 19 LYS cc_start: 0.7596 (tttt) cc_final: 0.7082 (tttm) REVERT: H 28 SER cc_start: 0.7901 (t) cc_final: 0.7683 (p) REVERT: H 73 ASP cc_start: 0.6656 (m-30) cc_final: 0.6242 (m-30) REVERT: H 109 ASP cc_start: 0.8117 (m-30) cc_final: 0.7379 (m-30) REVERT: B 4 MET cc_start: 0.6752 (mmm) cc_final: 0.5776 (mmm) REVERT: B 30 ARG cc_start: 0.7101 (mpt90) cc_final: 0.6867 (mmt-90) REVERT: B 42 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7792 (mt0) REVERT: B 47 MET cc_start: 0.6935 (mmp) cc_final: 0.6589 (mmp) REVERT: B 54 ARG cc_start: 0.8131 (ttm110) cc_final: 0.7781 (ttp80) REVERT: B 89 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.7006 (pt) REVERT: A 18 MET cc_start: 0.6345 (ttt) cc_final: 0.6038 (ttt) REVERT: A 19 LYS cc_start: 0.7404 (tttt) cc_final: 0.6775 (tttp) REVERT: A 25 SER cc_start: 0.6231 (m) cc_final: 0.5821 (p) REVERT: G 465 GLU cc_start: 0.7484 (tt0) cc_final: 0.7232 (tt0) outliers start: 29 outliers final: 26 residues processed: 121 average time/residue: 0.1966 time to fit residues: 30.2099 Evaluate side-chains 132 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 478 THR Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 43 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.127406 restraints weight = 6529.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131128 restraints weight = 3727.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.133702 restraints weight = 2515.076| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5147 Z= 0.194 Angle : 0.565 7.800 6975 Z= 0.292 Chirality : 0.044 0.200 754 Planarity : 0.004 0.060 891 Dihedral : 5.321 40.862 752 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 4.95 % Allowed : 20.15 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.80 (0.33), residues: 634 helix: -1.75 (1.35), residues: 15 sheet: -0.51 (0.33), residues: 243 loop : -1.69 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 111 HIS 0.005 0.001 HIS L 88 PHE 0.007 0.001 PHE B 62 TYR 0.019 0.001 TYR A 61 ARG 0.007 0.000 ARG G 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.34 seconds wall clock time: 35 minutes 45.28 seconds (2145.28 seconds total)