Starting phenix.real_space_refine on Fri Dec 27 18:25:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a7q_15224/12_2024/8a7q_15224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a7q_15224/12_2024/8a7q_15224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a7q_15224/12_2024/8a7q_15224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a7q_15224/12_2024/8a7q_15224.map" model { file = "/net/cci-nas-00/data/ceres_data/8a7q_15224/12_2024/8a7q_15224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a7q_15224/12_2024/8a7q_15224.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.002 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 36 5.16 5 C 4164 2.51 5 N 1020 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6492 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "B" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "C" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "D" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "E" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "G" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "H" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "I" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "J" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "L" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Time building chain proxies: 4.58, per 1000 atoms: 0.71 Number of scatterers: 6492 At special positions: 0 Unit cell: (147.58, 149.46, 33.84, 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 36 16.00 O 1272 8.00 N 1020 7.00 C 4164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 80 " distance=2.03 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS G 80 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 80 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 80 " distance=2.03 Simple disulfide: pdb=" SG CYS J 25 " - pdb=" SG CYS J 80 " distance=2.03 Simple disulfide: pdb=" SG CYS K 25 " - pdb=" SG CYS K 80 " distance=2.03 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 80 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 930.2 milliseconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 28 sheets defined 0.0% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 39 removed outlier: 6.872A pdb=" N ASP E 34 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP I 34 " --> pdb=" O SER E 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.579A pdb=" N VAL A 49 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 49 " --> pdb=" O GLU I 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 66 removed outlier: 6.989A pdb=" N TYR E 63 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU A 64 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU E 65 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR A 66 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR I 63 " --> pdb=" O PHE E 62 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU E 64 " --> pdb=" O TYR I 63 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU I 65 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR E 66 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA6, first strand: chain 'A' and resid 73 through 78 Processing sheet with id=AA7, first strand: chain 'A' and resid 81 through 83 Processing sheet with id=AA8, first strand: chain 'B' and resid 22 through 24 Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 39 removed outlier: 6.003A pdb=" N SER B 33 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLU F 36 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 35 " --> pdb=" O GLU F 36 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASP F 38 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 37 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER F 33 " --> pdb=" O ASP J 34 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLU J 36 " --> pdb=" O SER F 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE F 35 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP J 38 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL F 37 " --> pdb=" O ASP J 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 53 removed outlier: 9.434A pdb=" N LYS B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N HIS F 51 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU B 50 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ASP F 53 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER B 52 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N LYS F 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N HIS J 51 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU F 50 " --> pdb=" O HIS J 51 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ASP J 53 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER F 52 " --> pdb=" O ASP J 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 59 through 66 removed outlier: 6.984A pdb=" N TYR F 63 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 64 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU F 65 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR B 66 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR J 63 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU F 64 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU J 65 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR F 66 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AB4, first strand: chain 'B' and resid 74 through 78 removed outlier: 6.576A pdb=" N GLU B 74 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU F 77 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP B 76 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU F 74 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLU J 77 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASP F 76 " --> pdb=" O GLU J 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 81 through 83 removed outlier: 6.184A pdb=" N VAL B 82 " --> pdb=" O ASN F 83 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL F 82 " --> pdb=" O ASN J 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 22 through 24 removed outlier: 6.739A pdb=" N LEU C 23 " --> pdb=" O ASN G 24 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 33 through 39 removed outlier: 6.943A pdb=" N ASP G 34 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP K 34 " --> pdb=" O SER G 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 49 through 50 removed outlier: 6.533A pdb=" N VAL C 49 " --> pdb=" O GLU G 50 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL G 49 " --> pdb=" O GLU K 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 66 removed outlier: 7.023A pdb=" N TYR G 63 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU C 64 " --> pdb=" O TYR G 63 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU G 65 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N TYR C 66 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR K 63 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU G 64 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU K 65 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR G 66 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=AC2, first strand: chain 'C' and resid 73 through 78 removed outlier: 3.505A pdb=" N GLU G 74 " --> pdb=" O THR K 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 81 through 83 Processing sheet with id=AC4, first strand: chain 'D' and resid 22 through 24 Processing sheet with id=AC5, first strand: chain 'D' and resid 33 through 39 removed outlier: 5.937A pdb=" N SER D 33 " --> pdb=" O ASP H 34 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLU H 36 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE D 35 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASP H 38 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 37 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER H 33 " --> pdb=" O ASP L 34 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLU L 36 " --> pdb=" O SER H 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE H 35 " --> pdb=" O GLU L 36 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ASP L 38 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL H 37 " --> pdb=" O ASP L 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.601A pdb=" N VAL D 49 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER H 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LYS H 48 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N HIS L 51 " --> pdb=" O LYS H 48 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU H 50 " --> pdb=" O HIS L 51 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP L 53 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER H 52 " --> pdb=" O ASP L 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 59 through 66 removed outlier: 6.966A pdb=" N TYR H 63 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU D 64 " --> pdb=" O TYR H 63 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU H 65 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR D 66 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR L 63 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU H 64 " --> pdb=" O TYR L 63 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU L 65 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TYR H 66 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 69 through 70 Processing sheet with id=AC9, first strand: chain 'D' and resid 74 through 78 removed outlier: 6.565A pdb=" N GLU D 74 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLU H 77 " --> pdb=" O GLU D 74 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP D 76 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLU H 74 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLU L 77 " --> pdb=" O GLU H 74 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP H 76 " --> pdb=" O GLU L 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.088A pdb=" N VAL D 82 " --> pdb=" O ASN H 83 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL H 82 " --> pdb=" O ASN L 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 93 hydrogen bonds defined for protein. 279 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: 1.58 Time building geometry restraints manager: 1.85 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: 1974 1.34 - 1.46: 1269 1.46 - 1.57: 3393 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 6684 Sorted by residual: bond pdb=" N GLU G 77 " pdb=" CA GLU G 77 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.23e+00 bond pdb=" N GLU K 77 " pdb=" CA GLU K 77 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.21e-02 6.83e+03 7.04e+00 bond pdb=" N GLU A 77 " pdb=" CA GLU A 77 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N ASP G 76 " pdb=" CA ASP G 76 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.78e+00 bond pdb=" N GLU I 77 " pdb=" CA GLU I 77 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.21e-02 6.83e+03 6.68e+00 ... (remaining 6679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.89: 7909 0.89 - 1.77: 824 1.77 - 2.66: 217 2.66 - 3.54: 72 3.54 - 4.43: 14 Bond angle restraints: 9036 Sorted by residual: angle pdb=" CA ASP E 76 " pdb=" CB ASP E 76 " pdb=" CG ASP E 76 " ideal model delta sigma weight residual 112.60 117.03 -4.43 1.00e+00 1.00e+00 1.96e+01 angle pdb=" CA ASP I 76 " pdb=" CB ASP I 76 " pdb=" CG ASP I 76 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" CA ASP K 76 " pdb=" CB ASP K 76 " pdb=" CG ASP K 76 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" CA ASP A 76 " pdb=" CB ASP A 76 " pdb=" CG ASP A 76 " ideal model delta sigma weight residual 112.60 116.96 -4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" CA ASP C 76 " pdb=" CB ASP C 76 " pdb=" CG ASP C 76 " ideal model delta sigma weight residual 112.60 116.92 -4.32 1.00e+00 1.00e+00 1.87e+01 ... (remaining 9031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 3690 17.02 - 34.05: 189 34.05 - 51.07: 24 51.07 - 68.09: 12 68.09 - 85.12: 9 Dihedral angle restraints: 3924 sinusoidal: 1620 harmonic: 2304 Sorted by residual: dihedral pdb=" CB GLU B 47 " pdb=" CG GLU B 47 " pdb=" CD GLU B 47 " pdb=" OE1 GLU B 47 " ideal model delta sinusoidal sigma weight residual 0.00 -85.12 85.12 1 3.00e+01 1.11e-03 9.76e+00 dihedral pdb=" CB GLU J 47 " pdb=" CG GLU J 47 " pdb=" CD GLU J 47 " pdb=" OE1 GLU J 47 " ideal model delta sinusoidal sigma weight residual 0.00 -85.09 85.09 1 3.00e+01 1.11e-03 9.75e+00 dihedral pdb=" CB GLU L 47 " pdb=" CG GLU L 47 " pdb=" CD GLU L 47 " pdb=" OE1 GLU L 47 " ideal model delta sinusoidal sigma weight residual 0.00 -85.09 85.09 1 3.00e+01 1.11e-03 9.75e+00 ... (remaining 3921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 635 0.043 - 0.087: 156 0.087 - 0.130: 88 0.130 - 0.174: 23 0.174 - 0.217: 10 Chirality restraints: 912 Sorted by residual: chirality pdb=" CA LYS B 75 " pdb=" N LYS B 75 " pdb=" C LYS B 75 " pdb=" CB LYS B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA LYS D 75 " pdb=" N LYS D 75 " pdb=" C LYS D 75 " pdb=" CB LYS D 75 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA LYS J 75 " pdb=" N LYS J 75 " pdb=" C LYS J 75 " pdb=" CB LYS J 75 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 909 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE L 70 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.13e+00 pdb=" C PHE L 70 " 0.018 2.00e-02 2.50e+03 pdb=" O PHE L 70 " -0.007 2.00e-02 2.50e+03 pdb=" N THR L 71 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 70 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.13e+00 pdb=" C PHE J 70 " -0.018 2.00e-02 2.50e+03 pdb=" O PHE J 70 " 0.007 2.00e-02 2.50e+03 pdb=" N THR J 71 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 70 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C PHE D 70 " 0.018 2.00e-02 2.50e+03 pdb=" O PHE D 70 " -0.007 2.00e-02 2.50e+03 pdb=" N THR D 71 " -0.006 2.00e-02 2.50e+03 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 275 2.74 - 3.28: 5580 3.28 - 3.82: 10221 3.82 - 4.36: 12070 4.36 - 4.90: 21788 Nonbonded interactions: 49934 Sorted by model distance: nonbonded pdb=" O LYS D 58 " pdb=" N LYS H 58 " model vdw 2.197 3.120 nonbonded pdb=" O LYS A 58 " pdb=" N LYS E 58 " model vdw 2.229 3.120 nonbonded pdb=" OE2 GLU F 44 " pdb=" NH2 ARG K 45 " model vdw 2.246 3.120 nonbonded pdb=" O LYS F 58 " pdb=" N LYS J 58 " model vdw 2.251 3.120 nonbonded pdb=" O LYS B 58 " pdb=" N LYS F 58 " model vdw 2.252 3.120 ... (remaining 49929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.920 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 : 0.004 0.033 6684 Z= 0.258 Angle : 0.673 4.426 9036 Z= 0.451 Chirality : 0.055 0.217 912 Planarity : 0.003 0.022 1164 Dihedral : 11.640 85.115 2400 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.05 (0.17), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.13), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP L 60 HIS 0.004 0.001 HIS L 31 PHE 0.009 0.001 PHE J 70 TYR 0.007 0.001 TYR H 63 ARG 0.001 0.000 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7174 (tmm160) REVERT: B 38 ASP cc_start: 0.7219 (p0) cc_final: 0.6481 (p0) REVERT: C 45 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7093 (tmm160) REVERT: D 38 ASP cc_start: 0.7311 (p0) cc_final: 0.6643 (p0) REVERT: H 38 ASP cc_start: 0.7238 (p0) cc_final: 0.6763 (p0) REVERT: J 27 MET cc_start: 0.7761 (ttt) cc_final: 0.7484 (ttt) REVERT: J 38 ASP cc_start: 0.7302 (p0) cc_final: 0.7083 (p0) REVERT: J 53 ASP cc_start: 0.8012 (t0) cc_final: 0.7677 (t0) REVERT: L 27 MET cc_start: 0.7790 (ttt) cc_final: 0.7503 (ttt) REVERT: L 38 ASP cc_start: 0.7561 (p0) cc_final: 0.7214 (p0) REVERT: L 53 ASP cc_start: 0.8006 (t0) cc_final: 0.7726 (t0) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 1.1532 time to fit residues: 455.2558 Evaluate side-chains 293 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 56 optimal weight: 0.0770 chunk 21 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 overall best weight: 11.8150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 24 ASN C 83 ASN D 24 ASN E 24 ASN ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 HIS H 24 ASN K 24 ASN ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 6684 Z= 0.511 Angle : 0.860 7.382 9036 Z= 0.455 Chirality : 0.049 0.169 912 Planarity : 0.004 0.041 1164 Dihedral : 5.360 15.117 840 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 6.42 % Allowed : 25.68 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.18), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.14), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 60 HIS 0.006 0.002 HIS A 31 PHE 0.017 0.002 PHE H 22 TYR 0.016 0.002 TYR B 66 ARG 0.009 0.001 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 314 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7175 (tmm160) REVERT: A 74 GLU cc_start: 0.4260 (mm-30) cc_final: 0.4048 (mm-30) REVERT: B 41 LYS cc_start: 0.5572 (OUTLIER) cc_final: 0.4725 (mppt) REVERT: B 48 LYS cc_start: 0.8101 (mttt) cc_final: 0.7755 (pmtt) REVERT: B 74 GLU cc_start: 0.4831 (mm-30) cc_final: 0.4609 (tp30) REVERT: C 45 ARG cc_start: 0.7862 (mtt180) cc_final: 0.7246 (tmm160) REVERT: D 41 LYS cc_start: 0.5504 (OUTLIER) cc_final: 0.4709 (mppt) REVERT: D 48 LYS cc_start: 0.7956 (mttt) cc_final: 0.7721 (pmtt) REVERT: D 74 GLU cc_start: 0.4817 (mm-30) cc_final: 0.4611 (tp30) REVERT: I 48 LYS cc_start: 0.5461 (OUTLIER) cc_final: 0.4330 (mmpt) REVERT: J 27 MET cc_start: 0.7809 (ttt) cc_final: 0.7550 (ttt) REVERT: K 48 LYS cc_start: 0.5381 (OUTLIER) cc_final: 0.4287 (mmpt) REVERT: L 27 MET cc_start: 0.7813 (ttt) cc_final: 0.7565 (ttt) outliers start: 47 outliers final: 15 residues processed: 325 average time/residue: 1.1419 time to fit residues: 388.7120 Evaluate side-chains 295 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 276 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 ASN I 51 HIS K 51 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6684 Z= 0.369 Angle : 0.813 10.046 9036 Z= 0.420 Chirality : 0.047 0.162 912 Planarity : 0.004 0.033 1164 Dihedral : 5.293 16.146 840 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 7.10 % Allowed : 27.19 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.19), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 60 HIS 0.004 0.001 HIS C 31 PHE 0.011 0.002 PHE I 22 TYR 0.008 0.001 TYR G 78 ARG 0.008 0.001 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 312 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7188 (tmm160) REVERT: B 41 LYS cc_start: 0.5401 (OUTLIER) cc_final: 0.4399 (pttm) REVERT: B 48 LYS cc_start: 0.8117 (mttt) cc_final: 0.7711 (pmtt) REVERT: B 58 LYS cc_start: 0.4385 (OUTLIER) cc_final: 0.3778 (pmtt) REVERT: C 45 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7193 (tmm160) REVERT: D 41 LYS cc_start: 0.5429 (OUTLIER) cc_final: 0.4469 (pttm) REVERT: D 48 LYS cc_start: 0.8016 (mttt) cc_final: 0.7750 (pmtt) REVERT: D 58 LYS cc_start: 0.4598 (OUTLIER) cc_final: 0.3879 (pmtt) REVERT: F 36 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6740 (tm-30) REVERT: F 38 ASP cc_start: 0.6888 (p0) cc_final: 0.6555 (p0) REVERT: I 48 LYS cc_start: 0.5456 (OUTLIER) cc_final: 0.4410 (mmpt) REVERT: J 27 MET cc_start: 0.7701 (ttt) cc_final: 0.7472 (ttt) REVERT: J 48 LYS cc_start: 0.5862 (OUTLIER) cc_final: 0.5619 (mmpt) REVERT: K 48 LYS cc_start: 0.5556 (OUTLIER) cc_final: 0.4518 (mmpt) REVERT: L 27 MET cc_start: 0.7734 (ttt) cc_final: 0.7500 (ttt) REVERT: L 48 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.5689 (mmpt) outliers start: 52 outliers final: 21 residues processed: 326 average time/residue: 1.1796 time to fit residues: 402.3313 Evaluate side-chains 306 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 62 optimal weight: 0.2980 chunk 18 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6684 Z= 0.221 Angle : 0.803 12.337 9036 Z= 0.397 Chirality : 0.046 0.142 912 Planarity : 0.004 0.035 1164 Dihedral : 5.029 15.578 840 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.23 % Allowed : 30.46 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP K 60 HIS 0.005 0.001 HIS A 31 PHE 0.024 0.001 PHE A 22 TYR 0.027 0.001 TYR B 66 ARG 0.009 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 325 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7753 (mtt180) cc_final: 0.7204 (tmm160) REVERT: B 48 LYS cc_start: 0.8020 (mttt) cc_final: 0.7360 (pmtt) REVERT: C 45 ARG cc_start: 0.7671 (mtt180) cc_final: 0.7273 (tmm160) REVERT: D 48 LYS cc_start: 0.7909 (mttt) cc_final: 0.7659 (pmtt) REVERT: F 38 ASP cc_start: 0.6787 (p0) cc_final: 0.6397 (p0) REVERT: J 27 MET cc_start: 0.7657 (ttt) cc_final: 0.7416 (ttt) REVERT: K 48 LYS cc_start: 0.5612 (OUTLIER) cc_final: 0.4538 (mmpt) REVERT: L 27 MET cc_start: 0.7671 (ttt) cc_final: 0.7426 (ttt) REVERT: L 38 ASP cc_start: 0.7594 (p0) cc_final: 0.7286 (p0) REVERT: L 48 LYS cc_start: 0.5893 (OUTLIER) cc_final: 0.4994 (mmpt) outliers start: 31 outliers final: 9 residues processed: 330 average time/residue: 1.1814 time to fit residues: 407.9872 Evaluate side-chains 305 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 294 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 51 optimal weight: 30.0000 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 20.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS ** I 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6684 Z= 0.313 Angle : 0.857 12.027 9036 Z= 0.431 Chirality : 0.047 0.252 912 Planarity : 0.004 0.039 1164 Dihedral : 5.276 19.463 840 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 5.74 % Allowed : 29.51 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 60 HIS 0.003 0.001 HIS D 31 PHE 0.010 0.002 PHE C 22 TYR 0.013 0.001 TYR G 66 ARG 0.010 0.001 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7582 (mtt180) cc_final: 0.6898 (tmm160) REVERT: B 41 LYS cc_start: 0.5315 (OUTLIER) cc_final: 0.4673 (pttm) REVERT: B 48 LYS cc_start: 0.8117 (mttt) cc_final: 0.7416 (pmtt) REVERT: C 45 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7349 (tmm160) REVERT: D 41 LYS cc_start: 0.5493 (OUTLIER) cc_final: 0.4648 (pttm) REVERT: D 48 LYS cc_start: 0.7973 (mttt) cc_final: 0.7710 (pmtt) REVERT: F 36 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6803 (tm-30) REVERT: F 38 ASP cc_start: 0.6560 (p0) cc_final: 0.6214 (OUTLIER) REVERT: I 48 LYS cc_start: 0.5576 (OUTLIER) cc_final: 0.4411 (mmpt) REVERT: J 27 MET cc_start: 0.7664 (ttt) cc_final: 0.7452 (ttt) REVERT: J 48 LYS cc_start: 0.5586 (OUTLIER) cc_final: 0.4627 (mmpt) REVERT: K 48 LYS cc_start: 0.5381 (OUTLIER) cc_final: 0.4422 (mmpt) REVERT: L 27 MET cc_start: 0.7669 (ttt) cc_final: 0.7451 (ttt) REVERT: L 38 ASP cc_start: 0.7584 (p0) cc_final: 0.7343 (p0) REVERT: L 48 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.4834 (mmpt) outliers start: 42 outliers final: 22 residues processed: 309 average time/residue: 1.2085 time to fit residues: 390.3165 Evaluate side-chains 312 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 285 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain K residue 34 ASP Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 57 optimal weight: 0.2980 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 36 optimal weight: 40.0000 chunk 67 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.7019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6684 Z= 0.237 Angle : 0.887 14.382 9036 Z= 0.430 Chirality : 0.046 0.142 912 Planarity : 0.004 0.043 1164 Dihedral : 5.145 18.165 840 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.96 % Allowed : 32.24 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 60 HIS 0.003 0.001 HIS G 31 PHE 0.026 0.001 PHE C 22 TYR 0.023 0.001 TYR D 66 ARG 0.012 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 307 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7650 (mtt180) cc_final: 0.7184 (tmm160) REVERT: A 74 GLU cc_start: 0.3847 (mm-30) cc_final: 0.3605 (tp30) REVERT: B 48 LYS cc_start: 0.8078 (mttt) cc_final: 0.7391 (pmtt) REVERT: C 69 GLU cc_start: 0.4759 (pm20) cc_final: 0.4492 (pm20) REVERT: D 48 LYS cc_start: 0.7912 (mttt) cc_final: 0.7527 (pmtt) REVERT: F 38 ASP cc_start: 0.6565 (p0) cc_final: 0.6356 (OUTLIER) REVERT: J 27 MET cc_start: 0.7637 (ttt) cc_final: 0.7421 (ttt) REVERT: J 48 LYS cc_start: 0.5669 (OUTLIER) cc_final: 0.4694 (mmpt) REVERT: K 48 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.4771 (mmpt) REVERT: L 27 MET cc_start: 0.7628 (ttt) cc_final: 0.7404 (ttt) REVERT: L 48 LYS cc_start: 0.5788 (OUTLIER) cc_final: 0.4811 (mmpt) outliers start: 29 outliers final: 18 residues processed: 314 average time/residue: 1.2560 time to fit residues: 412.5205 Evaluate side-chains 305 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 285 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 40.0000 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS F 51 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6684 Z= 0.341 Angle : 0.978 13.961 9036 Z= 0.483 Chirality : 0.048 0.183 912 Planarity : 0.005 0.082 1164 Dihedral : 5.370 19.616 840 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.23 % Allowed : 36.61 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 60 HIS 0.003 0.001 HIS G 31 PHE 0.015 0.001 PHE G 22 TYR 0.008 0.001 TYR F 78 ARG 0.011 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 294 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7162 (tmm160) REVERT: A 74 GLU cc_start: 0.3715 (mm-30) cc_final: 0.3485 (tp30) REVERT: B 48 LYS cc_start: 0.8138 (mttt) cc_final: 0.7427 (pmtt) REVERT: D 48 LYS cc_start: 0.7932 (mttt) cc_final: 0.7556 (pmtt) REVERT: F 36 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6663 (tm-30) REVERT: F 38 ASP cc_start: 0.6502 (p0) cc_final: 0.6173 (OUTLIER) REVERT: I 48 LYS cc_start: 0.5466 (OUTLIER) cc_final: 0.4297 (mmpt) REVERT: J 27 MET cc_start: 0.7647 (ttt) cc_final: 0.7444 (ttt) REVERT: J 48 LYS cc_start: 0.5623 (OUTLIER) cc_final: 0.4695 (mmpt) REVERT: K 48 LYS cc_start: 0.5632 (OUTLIER) cc_final: 0.4550 (mmpt) REVERT: L 48 LYS cc_start: 0.5599 (OUTLIER) cc_final: 0.4615 (mmpt) outliers start: 31 outliers final: 18 residues processed: 299 average time/residue: 1.2134 time to fit residues: 379.7057 Evaluate side-chains 303 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 282 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 overall best weight: 11.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 6684 Z= 0.533 Angle : 1.110 15.955 9036 Z= 0.552 Chirality : 0.052 0.180 912 Planarity : 0.005 0.073 1164 Dihedral : 5.998 20.502 840 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 5.87 % Allowed : 35.93 % Favored : 58.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 60 HIS 0.003 0.001 HIS C 51 PHE 0.026 0.002 PHE C 22 TYR 0.024 0.002 TYR C 66 ARG 0.012 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7157 (tmm160) REVERT: B 48 LYS cc_start: 0.8187 (mttt) cc_final: 0.7692 (pmtt) REVERT: C 45 ARG cc_start: 0.6330 (ppt170) cc_final: 0.5782 (ptm-80) REVERT: D 48 LYS cc_start: 0.7931 (mttt) cc_final: 0.7692 (pmtt) REVERT: F 38 ASP cc_start: 0.6594 (p0) cc_final: 0.6223 (p0) REVERT: K 48 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.4296 (mmpt) REVERT: L 48 LYS cc_start: 0.5468 (OUTLIER) cc_final: 0.4505 (mmpt) outliers start: 43 outliers final: 25 residues processed: 292 average time/residue: 1.2365 time to fit residues: 377.2161 Evaluate side-chains 294 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.7447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 6684 Z= 0.354 Angle : 1.120 16.752 9036 Z= 0.542 Chirality : 0.050 0.173 912 Planarity : 0.004 0.051 1164 Dihedral : 5.863 20.172 840 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.69 % Allowed : 36.89 % Favored : 59.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.16), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 60 HIS 0.003 0.001 HIS J 31 PHE 0.024 0.002 PHE C 22 TYR 0.012 0.001 TYR I 66 ARG 0.011 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 283 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7077 (tmm160) REVERT: B 48 LYS cc_start: 0.8109 (mttt) cc_final: 0.7499 (pmtt) REVERT: C 45 ARG cc_start: 0.6300 (ppt170) cc_final: 0.5964 (ptm-80) REVERT: D 41 LYS cc_start: 0.5469 (OUTLIER) cc_final: 0.4994 (pttm) REVERT: D 48 LYS cc_start: 0.7947 (mttt) cc_final: 0.7580 (pmtt) REVERT: F 36 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6692 (tm-30) REVERT: F 38 ASP cc_start: 0.6389 (p0) cc_final: 0.6182 (p0) REVERT: I 48 LYS cc_start: 0.5428 (OUTLIER) cc_final: 0.4327 (mmpt) REVERT: K 48 LYS cc_start: 0.5571 (OUTLIER) cc_final: 0.4640 (mmpt) REVERT: L 48 LYS cc_start: 0.5510 (OUTLIER) cc_final: 0.4651 (mmpt) outliers start: 27 outliers final: 18 residues processed: 291 average time/residue: 1.3326 time to fit residues: 405.1088 Evaluate side-chains 295 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 273 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 48 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.7499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 6684 Z= 0.395 Angle : 1.153 15.531 9036 Z= 0.567 Chirality : 0.050 0.186 912 Planarity : 0.005 0.053 1164 Dihedral : 5.944 21.887 840 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.28 % Allowed : 39.48 % Favored : 57.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 60 HIS 0.003 0.001 HIS J 31 PHE 0.025 0.002 PHE C 22 TYR 0.027 0.002 TYR A 66 ARG 0.012 0.001 ARG E 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7101 (tmm160) REVERT: B 48 LYS cc_start: 0.8154 (mttt) cc_final: 0.7493 (pmtt) REVERT: D 48 LYS cc_start: 0.7920 (mttt) cc_final: 0.7653 (pmtt) REVERT: E 76 ASP cc_start: 0.7238 (m-30) cc_final: 0.6995 (m-30) REVERT: F 36 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6576 (tm-30) REVERT: F 38 ASP cc_start: 0.6560 (p0) cc_final: 0.6305 (p0) REVERT: I 48 LYS cc_start: 0.5197 (OUTLIER) cc_final: 0.4080 (mmpt) REVERT: K 48 LYS cc_start: 0.5616 (OUTLIER) cc_final: 0.4713 (mmpt) outliers start: 24 outliers final: 17 residues processed: 281 average time/residue: 1.3364 time to fit residues: 392.1070 Evaluate side-chains 291 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 272 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 7 optimal weight: 0.2980 chunk 10 optimal weight: 10.0000 chunk 50 optimal weight: 0.2980 chunk 3 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.107905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.101991 restraints weight = 21471.627| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 3.66 r_work: 0.4092 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6684 Z= 0.291 Angle : 1.134 15.862 9036 Z= 0.554 Chirality : 0.048 0.168 912 Planarity : 0.004 0.050 1164 Dihedral : 5.687 21.303 840 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.19 % Allowed : 41.53 % Favored : 56.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.20), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.15), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP K 60 HIS 0.003 0.001 HIS G 31 PHE 0.024 0.001 PHE A 22 TYR 0.024 0.001 TYR C 66 ARG 0.011 0.001 ARG E 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5237.75 seconds wall clock time: 93 minutes 36.63 seconds (5616.63 seconds total)