Starting phenix.real_space_refine on Sat Nov 16 23:40:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f32_28829/11_2024/8f32_28829.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f32_28829/11_2024/8f32_28829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f32_28829/11_2024/8f32_28829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f32_28829/11_2024/8f32_28829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f32_28829/11_2024/8f32_28829.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f32_28829/11_2024/8f32_28829.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 8180 2.51 5 N 2085 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12545 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D Time building chain proxies: 5.20, per 1000 atoms: 0.41 Number of scatterers: 12545 At special positions: 0 Unit cell: (88.41, 88.41, 122.932, 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 30 16.00 O 2250 8.00 N 2085 7.00 C 8180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.6 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 31.9% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.633A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 209 through 222 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 227 through 248 removed outlier: 3.626A pdb=" N ARG E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 286 Processing helix chain 'E' and resid 303 through 317 Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.633A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 209 through 222 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 227 through 248 removed outlier: 3.626A pdb=" N ARG D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 286 Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.633A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 209 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 227 through 248 removed outlier: 3.626A pdb=" N ARG C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 286 Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.634A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 209 through 222 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 227 through 248 removed outlier: 3.626A pdb=" N ARG B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 286 Processing helix chain 'B' and resid 303 through 317 Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.634A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 209 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 227 through 248 removed outlier: 3.627A pdb=" N ARG A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 286 Processing helix chain 'A' and resid 303 through 317 Processing sheet with id=AA1, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.717A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.085A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.569A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP E 196 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS E 165 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL E 198 " --> pdb=" O ARG E 163 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG E 163 " --> pdb=" O VAL E 198 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.717A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.085A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.569A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP D 196 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS D 165 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL D 198 " --> pdb=" O ARG D 163 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG D 163 " --> pdb=" O VAL D 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 4.718A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.085A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.569A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP C 196 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS C 165 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 198 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG C 163 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 58 removed outlier: 4.716A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.085A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.570A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP B 196 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS B 165 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL B 198 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG B 163 " --> pdb=" O VAL B 198 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.717A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.085A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.569A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP A 196 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS A 165 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 198 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG A 163 " --> pdb=" O VAL A 198 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1800 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: 3.65 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3475 1.33 - 1.45: 2400 1.45 - 1.57: 6955 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12880 Sorted by residual: bond pdb=" CB GLU B 150 " pdb=" CG GLU B 150 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.40e+00 bond pdb=" CB GLU C 150 " pdb=" CG GLU C 150 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.39e+00 bond pdb=" CB GLU E 150 " pdb=" CG GLU E 150 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.38e+00 bond pdb=" CB GLU D 150 " pdb=" CG GLU D 150 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.37e+00 bond pdb=" CB GLU A 150 " pdb=" CG GLU A 150 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.37e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 16589 1.59 - 3.17: 759 3.17 - 4.76: 112 4.76 - 6.34: 65 6.34 - 7.93: 20 Bond angle restraints: 17545 Sorted by residual: angle pdb=" N ILE C 157 " pdb=" CA ILE C 157 " pdb=" C ILE C 157 " ideal model delta sigma weight residual 113.71 106.87 6.84 9.50e-01 1.11e+00 5.19e+01 angle pdb=" N ILE D 157 " pdb=" CA ILE D 157 " pdb=" C ILE D 157 " ideal model delta sigma weight residual 113.71 106.87 6.84 9.50e-01 1.11e+00 5.18e+01 angle pdb=" N ILE B 157 " pdb=" CA ILE B 157 " pdb=" C ILE B 157 " ideal model delta sigma weight residual 113.71 106.88 6.83 9.50e-01 1.11e+00 5.18e+01 angle pdb=" N ILE E 157 " pdb=" CA ILE E 157 " pdb=" C ILE E 157 " ideal model delta sigma weight residual 113.71 106.88 6.83 9.50e-01 1.11e+00 5.17e+01 angle pdb=" N ILE A 157 " pdb=" CA ILE A 157 " pdb=" C ILE A 157 " ideal model delta sigma weight residual 113.71 106.89 6.82 9.50e-01 1.11e+00 5.16e+01 ... (remaining 17540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 6455 14.33 - 28.66: 855 28.66 - 42.99: 185 42.99 - 57.32: 20 57.32 - 71.65: 15 Dihedral angle restraints: 7530 sinusoidal: 3025 harmonic: 4505 Sorted by residual: dihedral pdb=" CA SER D 227 " pdb=" C SER D 227 " pdb=" N PHE D 228 " pdb=" CA PHE D 228 " ideal model delta harmonic sigma weight residual 180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA SER A 227 " pdb=" C SER A 227 " pdb=" N PHE A 228 " pdb=" CA PHE A 228 " ideal model delta harmonic sigma weight residual -180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA SER B 227 " pdb=" C SER B 227 " pdb=" N PHE B 228 " pdb=" CA PHE B 228 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1184 0.043 - 0.086: 515 0.086 - 0.130: 206 0.130 - 0.173: 40 0.173 - 0.216: 5 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CB ILE B 39 " pdb=" CA ILE B 39 " pdb=" CG1 ILE B 39 " pdb=" CG2 ILE B 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE D 39 " pdb=" CA ILE D 39 " pdb=" CG1 ILE D 39 " pdb=" CG2 ILE D 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE C 39 " pdb=" CA ILE C 39 " pdb=" CG1 ILE C 39 " pdb=" CG2 ILE C 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1947 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 119 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO D 120 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 120 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 120 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 119 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO E 120 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 120 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 120 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 119 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO A 120 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 120 " 0.028 5.00e-02 4.00e+02 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 960 2.74 - 3.28: 12129 3.28 - 3.82: 20409 3.82 - 4.36: 24824 4.36 - 4.90: 43288 Nonbonded interactions: 101610 Sorted by model distance: nonbonded pdb=" OG SER D 227 " pdb=" OE2 GLU D 230 " model vdw 2.201 3.040 nonbonded pdb=" OG SER C 227 " pdb=" OE2 GLU C 230 " model vdw 2.201 3.040 nonbonded pdb=" OG SER E 227 " pdb=" OE2 GLU E 230 " model vdw 2.202 3.040 nonbonded pdb=" OG SER A 227 " pdb=" OE2 GLU A 230 " model vdw 2.202 3.040 nonbonded pdb=" OG SER B 227 " pdb=" OE2 GLU B 230 " model vdw 2.202 3.040 ... (remaining 101605 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 26.620 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 0.049 12880 Z= 0.302 Angle : 0.837 7.926 17545 Z= 0.467 Chirality : 0.056 0.216 1950 Planarity : 0.006 0.050 2235 Dihedral : 13.435 71.655 4620 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: -1.60 (0.21), residues: 1525 helix: -0.87 (0.22), residues: 525 sheet: -0.04 (0.23), residues: 490 loop : -2.13 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 43 HIS 0.013 0.003 HIS C 169 PHE 0.018 0.002 PHE B 308 TYR 0.020 0.002 TYR D 245 ARG 0.003 0.000 ARG C 286 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: E 187 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6593 (tm-30) REVERT: D 86 ASP cc_start: 0.6982 (t70) cc_final: 0.6574 (t0) REVERT: C 86 ASP cc_start: 0.7052 (t70) cc_final: 0.6644 (t0) REVERT: C 115 ASP cc_start: 0.6719 (t0) cc_final: 0.5810 (t0) REVERT: C 117 ARG cc_start: 0.7805 (mmt180) cc_final: 0.7204 (mmt180) REVERT: C 187 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6710 (tm-30) REVERT: B 86 ASP cc_start: 0.6869 (t70) cc_final: 0.6406 (t0) REVERT: B 187 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6651 (tm-30) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2531 time to fit residues: 99.9158 Evaluate side-chains 202 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 42 GLN E 146 GLN E 177 HIS D 21 ASN D 146 GLN D 169 HIS C 60 ASN C 146 GLN C 177 HIS B 21 ASN B 62 GLN B 139 GLN B 146 GLN A 21 ASN A 42 GLN A 139 GLN A 146 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12880 Z= 0.370 Angle : 0.632 5.706 17545 Z= 0.337 Chirality : 0.049 0.138 1950 Planarity : 0.005 0.045 2235 Dihedral : 5.301 25.146 1690 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.67 % Allowed : 11.93 % Favored : 86.40 % 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: -0.77 (0.22), residues: 1525 helix: 0.71 (0.24), residues: 495 sheet: -0.24 (0.23), residues: 475 loop : -1.83 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 43 HIS 0.007 0.002 HIS B 169 PHE 0.024 0.002 PHE B 19 TYR 0.012 0.002 TYR B 258 ARG 0.003 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: D 86 ASP cc_start: 0.6934 (t70) cc_final: 0.6481 (t0) outliers start: 23 outliers final: 19 residues processed: 211 average time/residue: 0.2542 time to fit residues: 77.6271 Evaluate side-chains 197 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 266 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN D 177 HIS C 60 ASN B 177 HIS A 89 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12880 Z= 0.218 Angle : 0.520 4.852 17545 Z= 0.276 Chirality : 0.046 0.133 1950 Planarity : 0.004 0.046 2235 Dihedral : 4.768 20.358 1690 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.62 % Allowed : 14.84 % Favored : 82.55 % 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: -0.25 (0.22), residues: 1525 helix: 1.39 (0.25), residues: 495 sheet: 0.06 (0.23), residues: 455 loop : -1.73 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 43 HIS 0.006 0.001 HIS B 169 PHE 0.021 0.001 PHE A 19 TYR 0.008 0.001 TYR D 245 ARG 0.003 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 264 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6966 (mp10) outliers start: 36 outliers final: 23 residues processed: 222 average time/residue: 0.2493 time to fit residues: 80.2167 Evaluate side-chains 195 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 266 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12880 Z= 0.265 Angle : 0.538 4.717 17545 Z= 0.286 Chirality : 0.047 0.131 1950 Planarity : 0.004 0.040 2235 Dihedral : 4.702 21.649 1690 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.71 % Allowed : 14.69 % Favored : 81.60 % 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: -0.21 (0.22), residues: 1525 helix: 1.50 (0.25), residues: 495 sheet: -0.02 (0.23), residues: 465 loop : -1.74 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 43 HIS 0.008 0.002 HIS B 169 PHE 0.024 0.002 PHE B 19 TYR 0.009 0.002 TYR C 245 ARG 0.003 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 1.262 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: symmetry clash outliers start: 51 outliers final: 39 residues processed: 221 average time/residue: 0.2506 time to fit residues: 81.0208 Evaluate side-chains 216 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 266 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 0.0470 chunk 130 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN C 60 ASN B 42 GLN A 177 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12880 Z= 0.191 Angle : 0.496 4.576 17545 Z= 0.262 Chirality : 0.045 0.131 1950 Planarity : 0.003 0.034 2235 Dihedral : 4.431 18.815 1690 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.29 % Allowed : 15.05 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1525 helix: 1.80 (0.25), residues: 490 sheet: 0.01 (0.23), residues: 465 loop : -1.68 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 43 HIS 0.009 0.002 HIS B 169 PHE 0.018 0.001 PHE B 19 TYR 0.007 0.001 TYR A 245 ARG 0.003 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 1.510 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: symmetry clash outliers start: 59 outliers final: 39 residues processed: 229 average time/residue: 0.2443 time to fit residues: 82.1810 Evaluate side-chains 212 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 139 optimal weight: 0.0070 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 60 ASN D 89 ASN C 21 ASN C 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12880 Z= 0.261 Angle : 0.539 5.305 17545 Z= 0.283 Chirality : 0.046 0.132 1950 Planarity : 0.003 0.034 2235 Dihedral : 4.542 20.911 1690 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.87 % Allowed : 15.13 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1525 helix: 1.78 (0.25), residues: 490 sheet: -0.02 (0.23), residues: 465 loop : -1.72 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 43 HIS 0.010 0.002 HIS B 169 PHE 0.017 0.001 PHE A 19 TYR 0.009 0.001 TYR E 245 ARG 0.002 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 187 time to evaluate : 1.430 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: symmetry clash revert: symmetry clash REVERT: D 22 LYS cc_start: 0.8578 (pttm) cc_final: 0.8125 (pttm) REVERT: A 54 LYS cc_start: 0.7506 (mmtt) cc_final: 0.7243 (tppt) REVERT: A 255 ARG cc_start: 0.6727 (mmt-90) cc_final: 0.6395 (mtt-85) outliers start: 67 outliers final: 54 residues processed: 226 average time/residue: 0.2409 time to fit residues: 79.5435 Evaluate side-chains 228 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 174 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 144 optimal weight: 0.0370 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN C 60 ASN A 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12880 Z= 0.214 Angle : 0.520 7.174 17545 Z= 0.271 Chirality : 0.046 0.134 1950 Planarity : 0.003 0.034 2235 Dihedral : 4.416 19.001 1690 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.44 % Allowed : 16.15 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.22), residues: 1525 helix: 1.85 (0.25), residues: 490 sheet: 0.02 (0.23), residues: 465 loop : -1.69 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 43 HIS 0.009 0.002 HIS B 169 PHE 0.015 0.001 PHE A 19 TYR 0.007 0.001 TYR D 245 ARG 0.002 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 ASP cc_start: 0.6911 (p0) cc_final: 0.6687 (p0) REVERT: C 223 PHE cc_start: 0.8125 (m-80) cc_final: 0.7899 (m-80) REVERT: A 54 LYS cc_start: 0.7454 (mmtt) cc_final: 0.7196 (tppt) REVERT: A 255 ARG cc_start: 0.6755 (mmt-90) cc_final: 0.6453 (mtt-85) outliers start: 61 outliers final: 53 residues processed: 229 average time/residue: 0.2352 time to fit residues: 79.5644 Evaluate side-chains 230 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 0.0670 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 0.0770 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.9078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN A 60 ASN A 89 ASN A 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12880 Z= 0.163 Angle : 0.495 6.189 17545 Z= 0.258 Chirality : 0.045 0.148 1950 Planarity : 0.003 0.034 2235 Dihedral : 4.230 16.323 1690 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.07 % Allowed : 16.73 % Favored : 79.20 % 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: 0.14 (0.23), residues: 1525 helix: 1.93 (0.25), residues: 490 sheet: 0.17 (0.24), residues: 465 loop : -1.63 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 43 HIS 0.011 0.002 HIS B 169 PHE 0.020 0.001 PHE E 236 TYR 0.007 0.001 TYR C 245 ARG 0.004 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 ASP cc_start: 0.6858 (p0) cc_final: 0.6651 (p0) REVERT: E 237 THR cc_start: 0.8506 (m) cc_final: 0.8298 (m) REVERT: E 255 ARG cc_start: 0.6516 (mtt90) cc_final: 0.6045 (mtt-85) REVERT: D 113 ASP cc_start: 0.7070 (p0) cc_final: 0.6865 (p0) REVERT: D 255 ARG cc_start: 0.6821 (mpt90) cc_final: 0.6326 (mtt-85) REVERT: A 54 LYS cc_start: 0.7380 (mmtt) cc_final: 0.7111 (tppt) outliers start: 56 outliers final: 46 residues processed: 244 average time/residue: 0.2593 time to fit residues: 93.6719 Evaluate side-chains 230 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 0.0570 chunk 142 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN A 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12880 Z= 0.177 Angle : 0.526 8.987 17545 Z= 0.272 Chirality : 0.045 0.184 1950 Planarity : 0.003 0.033 2235 Dihedral : 4.206 16.769 1690 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.00 % Allowed : 17.24 % Favored : 78.76 % 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: 0.21 (0.23), residues: 1525 helix: 1.93 (0.25), residues: 490 sheet: 0.24 (0.24), residues: 465 loop : -1.58 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 43 HIS 0.010 0.001 HIS B 169 PHE 0.026 0.001 PHE B 19 TYR 0.006 0.001 TYR C 24 ARG 0.004 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 ASP cc_start: 0.6851 (p0) cc_final: 0.6646 (p0) REVERT: E 255 ARG cc_start: 0.6541 (mpt90) cc_final: 0.6069 (mtt-85) REVERT: D 255 ARG cc_start: 0.6804 (mpt90) cc_final: 0.6334 (mtt-85) REVERT: D 264 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6877 (mp10) REVERT: B 255 ARG cc_start: 0.6552 (mpt90) cc_final: 0.6158 (mtt-85) REVERT: A 54 LYS cc_start: 0.7366 (mmtt) cc_final: 0.7096 (tppt) outliers start: 55 outliers final: 50 residues processed: 214 average time/residue: 0.2413 time to fit residues: 75.4715 Evaluate side-chains 231 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 94 optimal weight: 0.1980 chunk 126 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN A 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12880 Z= 0.267 Angle : 0.569 10.208 17545 Z= 0.296 Chirality : 0.047 0.188 1950 Planarity : 0.003 0.033 2235 Dihedral : 4.434 20.945 1690 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.07 % Allowed : 16.95 % Favored : 78.98 % 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: 0.11 (0.23), residues: 1525 helix: 1.87 (0.25), residues: 490 sheet: 0.15 (0.24), residues: 465 loop : -1.63 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 160 HIS 0.010 0.001 HIS B 169 PHE 0.024 0.002 PHE B 19 TYR 0.013 0.001 TYR D 245 ARG 0.005 0.000 ARG C 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 185 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 ASP cc_start: 0.6919 (p0) cc_final: 0.6712 (p0) REVERT: E 255 ARG cc_start: 0.6586 (mpt90) cc_final: 0.6095 (mtt-85) REVERT: B 230 GLU cc_start: 0.7181 (pm20) cc_final: 0.6604 (pt0) REVERT: A 54 LYS cc_start: 0.7442 (mmtt) cc_final: 0.7140 (tppt) outliers start: 56 outliers final: 50 residues processed: 217 average time/residue: 0.2420 time to fit residues: 76.9626 Evaluate side-chains 225 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN D 89 ASN A 60 ASN A 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.150379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.119469 restraints weight = 17025.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.123286 restraints weight = 10732.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.125841 restraints weight = 7953.392| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 12880 Z= 0.274 Angle : 0.810 59.091 17545 Z= 0.467 Chirality : 0.051 0.973 1950 Planarity : 0.004 0.059 2235 Dihedral : 4.489 28.340 1690 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.07 % Rotamer: Outliers : 3.93 % Allowed : 17.24 % Favored : 78.84 % Cbeta Deviations : 0.07 % 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: 0.10 (0.23), residues: 1525 helix: 1.87 (0.25), residues: 490 sheet: 0.14 (0.24), residues: 465 loop : -1.64 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 224 HIS 0.008 0.001 HIS B 169 PHE 0.023 0.002 PHE B 19 TYR 0.014 0.001 TYR E 245 ARG 0.025 0.000 ARG B 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2443.62 seconds wall clock time: 45 minutes 32.19 seconds (2732.19 seconds total)