Starting phenix.real_space_refine on Sat Dec 28 19:33:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wur_32839/12_2024/7wur_32839.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wur_32839/12_2024/7wur_32839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wur_32839/12_2024/7wur_32839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wur_32839/12_2024/7wur_32839.map" model { file = "/net/cci-nas-00/data/ceres_data/7wur_32839/12_2024/7wur_32839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wur_32839/12_2024/7wur_32839.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 336 atoms to isotropic. 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 52 5.16 5 C 5636 2.51 5 N 1528 2.21 5 O 1706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 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: 8922 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2725 Classifications: {'peptide': 341} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 321} Chain: "B" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2725 Classifications: {'peptide': 341} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 321} Chain: "E" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "F" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "G" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "H" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Time building chain proxies: 5.58, per 1000 atoms: 0.63 Number of scatterers: 8922 At special positions: 0 Unit cell: (84.48, 109.56, 162.36, 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 52 16.00 O 1706 8.00 N 1528 7.00 C 5636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " 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: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 20 sheets defined 12.8% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.759A pdb=" N LEU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 82 removed outlier: 3.808A pdb=" N ASN A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Proline residue: A 73 - end of helix removed outlier: 3.637A pdb=" N HIS A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.592A pdb=" N HIS A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.501A pdb=" N ASN A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 removed outlier: 3.675A pdb=" N LEU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.749A pdb=" N ASN B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.552A pdb=" N HIS B 229 " --> pdb=" O PRO B 226 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.561A pdb=" N ASN B 255 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.665A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.716A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.670A pdb=" N THR E 91 " --> pdb=" O ASP E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.841A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.815A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.822A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.899A pdb=" N PHE H 84 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.598A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 89 removed outlier: 3.642A pdb=" N MET A 89 " --> pdb=" O PHE A 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.366A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE A 212 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ALA A 205 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 216 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 216 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ALA B 205 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE B 212 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 287 removed outlier: 5.996A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N CYS A 313 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 88 through 89 removed outlier: 3.563A pdb=" N MET B 89 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287 removed outlier: 5.990A pdb=" N THR B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N CYS B 313 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.089A pdb=" N TYR E 107 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY E 109 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N CYS E 96 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY E 111 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N TYR E 94 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU E 113 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA E 92 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.601A pdb=" N ASP F 71 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.135A pdb=" N TYR G 107 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY G 109 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS G 96 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY G 111 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TYR G 94 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU G 113 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ALA G 92 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.680A pdb=" N PHE H 72 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA H 19 " --> pdb=" O ILE H 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.680A pdb=" N PHE H 72 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP H 71 " --> pdb=" O SER H 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.247A pdb=" N LEU H 11 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR H 87 " --> pdb=" O THR H 104 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 564 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: 2.64 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2870 1.34 - 1.46: 2341 1.46 - 1.58: 3867 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 9150 Sorted by residual: bond pdb=" N GLN B 107 " pdb=" CA GLN B 107 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" N GLN A 107 " pdb=" CA GLN A 107 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.44e+00 bond pdb=" CA ILE B 243 " pdb=" CB ILE B 243 " ideal model delta sigma weight residual 1.540 1.522 0.018 1.23e-02 6.61e+03 2.11e+00 bond pdb=" CB GLN A 70 " pdb=" CG GLN A 70 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.80e+00 bond pdb=" C PRO A 106 " pdb=" N GLN A 107 " ideal model delta sigma weight residual 1.329 1.347 -0.018 1.40e-02 5.10e+03 1.71e+00 ... (remaining 9145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 12279 2.65 - 5.30: 111 5.30 - 7.95: 11 7.95 - 10.60: 5 10.60 - 13.25: 4 Bond angle restraints: 12410 Sorted by residual: angle pdb=" C PRO B 106 " pdb=" N GLN B 107 " pdb=" CA GLN B 107 " ideal model delta sigma weight residual 121.70 133.13 -11.43 1.80e+00 3.09e-01 4.03e+01 angle pdb=" C PRO A 106 " pdb=" N GLN A 107 " pdb=" CA GLN A 107 " ideal model delta sigma weight residual 121.70 132.97 -11.27 1.80e+00 3.09e-01 3.92e+01 angle pdb=" CB MET E 34 " pdb=" CG MET E 34 " pdb=" SD MET E 34 " ideal model delta sigma weight residual 112.70 125.95 -13.25 3.00e+00 1.11e-01 1.95e+01 angle pdb=" CA GLN A 70 " pdb=" CB GLN A 70 " pdb=" CG GLN A 70 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CB MET B 198 " pdb=" CG MET B 198 " pdb=" SD MET B 198 " ideal model delta sigma weight residual 112.70 124.65 -11.95 3.00e+00 1.11e-01 1.59e+01 ... (remaining 12405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 4831 17.32 - 34.64: 478 34.64 - 51.97: 97 51.97 - 69.29: 6 69.29 - 86.61: 14 Dihedral angle restraints: 5426 sinusoidal: 2178 harmonic: 3248 Sorted by residual: dihedral pdb=" CA LYS A 33 " pdb=" C LYS A 33 " pdb=" N PHE A 34 " pdb=" CA PHE A 34 " ideal model delta harmonic sigma weight residual 180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " pdb=" SG CYS B 143 " pdb=" CB CYS B 143 " ideal model delta sinusoidal sigma weight residual -86.00 -123.21 37.21 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CA LYS A 189 " pdb=" C LYS A 189 " pdb=" N ASP A 190 " pdb=" CA ASP A 190 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1080 0.049 - 0.097: 177 0.097 - 0.146: 71 0.146 - 0.194: 0 0.194 - 0.243: 2 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CA GLN A 107 " pdb=" N GLN A 107 " pdb=" C GLN A 107 " pdb=" CB GLN A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA GLN B 107 " pdb=" N GLN B 107 " pdb=" C GLN B 107 " pdb=" CB GLN B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLN E 110 " pdb=" N GLN E 110 " pdb=" C GLN E 110 " pdb=" CB GLN E 110 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 1327 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 20 " -0.010 2.00e-02 2.50e+03 1.30e-02 2.96e+00 pdb=" CG PHE B 20 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 20 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 20 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 20 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 20 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 20 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 70 " 0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C GLN A 70 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN A 70 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 71 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 72 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 73 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " 0.020 5.00e-02 4.00e+02 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 925 2.75 - 3.29: 8826 3.29 - 3.82: 14527 3.82 - 4.36: 17416 4.36 - 4.90: 29740 Nonbonded interactions: 71434 Sorted by model distance: nonbonded pdb=" OE2 GLU A 281 " pdb=" OG SER E 52 " model vdw 2.211 3.040 nonbonded pdb=" OE2 GLU B 281 " pdb=" OG SER G 52 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR A 288 " pdb=" OD1 ASP A 290 " model vdw 2.242 3.040 nonbonded pdb=" N GLU E 89 " pdb=" OE1 GLU E 89 " model vdw 2.245 3.120 nonbonded pdb=" OG SER B 103 " pdb=" OE1 GLN B 175 " model vdw 2.247 3.040 ... (remaining 71429 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' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.380 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9150 Z= 0.177 Angle : 0.680 13.252 12410 Z= 0.386 Chirality : 0.043 0.243 1330 Planarity : 0.003 0.035 1578 Dihedral : 14.344 86.610 3306 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.31 % Allowed : 9.86 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.48 (0.26), residues: 1122 helix: -1.02 (0.57), residues: 68 sheet: -0.59 (0.29), residues: 360 loop : -1.20 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 108 HIS 0.001 0.000 HIS B 229 PHE 0.030 0.001 PHE B 20 TYR 0.011 0.001 TYR B 32 ARG 0.003 0.000 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8624 (tpp) cc_final: 0.8311 (tpt) REVERT: A 333 MET cc_start: 0.8411 (mmm) cc_final: 0.7856 (mtt) REVERT: E 110 GLN cc_start: 0.8508 (mp10) cc_final: 0.7686 (pp30) outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 0.2100 time to fit residues: 20.7762 Evaluate side-chains 67 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain F residue 3 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9150 Z= 0.173 Angle : 0.625 12.048 12410 Z= 0.330 Chirality : 0.043 0.231 1330 Planarity : 0.004 0.030 1578 Dihedral : 4.873 47.988 1237 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.82 % Allowed : 9.86 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.39 (0.26), residues: 1122 helix: -0.33 (0.59), residues: 72 sheet: -0.43 (0.29), residues: 348 loop : -1.27 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 108 HIS 0.002 0.000 HIS B 195 PHE 0.018 0.001 PHE B 34 TYR 0.010 0.001 TYR B 32 ARG 0.003 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: B 174 ARG cc_start: 0.8625 (ptp90) cc_final: 0.8113 (pmt-80) REVERT: B 272 ARG cc_start: 0.8532 (mtt90) cc_final: 0.8234 (ttm110) outliers start: 8 outliers final: 3 residues processed: 73 average time/residue: 0.2236 time to fit residues: 23.2773 Evaluate side-chains 68 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.0030 chunk 83 optimal weight: 0.3980 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 0.0470 chunk 80 optimal weight: 0.6980 overall best weight: 0.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9150 Z= 0.147 Angle : 0.593 11.849 12410 Z= 0.310 Chirality : 0.043 0.236 1330 Planarity : 0.003 0.031 1578 Dihedral : 4.621 57.292 1234 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.62 % Allowed : 11.81 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.38 (0.26), residues: 1122 helix: -0.07 (0.59), residues: 72 sheet: -0.48 (0.30), residues: 330 loop : -1.25 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 108 HIS 0.001 0.000 HIS A 26 PHE 0.012 0.001 PHE B 34 TYR 0.008 0.001 TYR E 33 ARG 0.002 0.000 ARG F 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.9023 (pm20) cc_final: 0.8659 (pm20) REVERT: A 68 TRP cc_start: 0.9386 (m100) cc_final: 0.8992 (m100) REVERT: A 184 MET cc_start: 0.8004 (tpt) cc_final: 0.7682 (ttt) REVERT: B 35 GLN cc_start: 0.8647 (mp10) cc_final: 0.8090 (mp10) REVERT: B 67 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8234 (tpp) REVERT: B 174 ARG cc_start: 0.8612 (ptp90) cc_final: 0.8149 (pmt-80) REVERT: B 272 ARG cc_start: 0.8456 (mtt90) cc_final: 0.8015 (ttm110) REVERT: E 59 ASP cc_start: 0.7943 (t0) cc_final: 0.7740 (t0) REVERT: E 110 GLN cc_start: 0.8626 (mp10) cc_final: 0.7818 (pp30) REVERT: G 3 GLN cc_start: 0.8286 (mp10) cc_final: 0.7942 (mp10) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.2171 time to fit residues: 23.8205 Evaluate side-chains 74 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.0980 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN B 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9150 Z= 0.204 Angle : 0.606 11.864 12410 Z= 0.315 Chirality : 0.042 0.230 1330 Planarity : 0.003 0.028 1578 Dihedral : 4.620 51.179 1233 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.13 % Allowed : 12.42 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.29 (0.26), residues: 1122 helix: 0.35 (0.61), residues: 72 sheet: -0.59 (0.29), residues: 362 loop : -1.14 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 108 HIS 0.003 0.001 HIS B 195 PHE 0.022 0.001 PHE B 20 TYR 0.008 0.001 TYR H 50 ARG 0.002 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.9018 (pm20) cc_final: 0.8695 (pm20) REVERT: A 68 TRP cc_start: 0.9427 (m100) cc_final: 0.9039 (m100) REVERT: B 35 GLN cc_start: 0.8584 (mp10) cc_final: 0.7976 (mp10) REVERT: B 67 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8028 (tmm) REVERT: B 174 ARG cc_start: 0.8685 (ptp90) cc_final: 0.8143 (pmt-80) REVERT: B 272 ARG cc_start: 0.8490 (mtt90) cc_final: 0.8128 (ttm110) REVERT: E 59 ASP cc_start: 0.8326 (t0) cc_final: 0.8046 (t0) REVERT: G 1 GLN cc_start: 0.8391 (tp40) cc_final: 0.8178 (pm20) REVERT: G 3 GLN cc_start: 0.8241 (mp10) cc_final: 0.7616 (mp10) REVERT: G 59 ASP cc_start: 0.8909 (t0) cc_final: 0.8447 (t0) outliers start: 11 outliers final: 5 residues processed: 75 average time/residue: 0.2325 time to fit residues: 24.4356 Evaluate side-chains 72 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9150 Z= 0.314 Angle : 0.653 11.915 12410 Z= 0.339 Chirality : 0.043 0.235 1330 Planarity : 0.003 0.028 1578 Dihedral : 4.883 45.241 1233 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.44 % Allowed : 13.14 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.35 (0.26), residues: 1122 helix: 0.49 (0.59), residues: 76 sheet: -0.68 (0.30), residues: 340 loop : -1.18 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 108 HIS 0.004 0.001 HIS B 195 PHE 0.017 0.001 PHE A 34 TYR 0.013 0.001 TYR H 87 ARG 0.006 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.9025 (pm20) cc_final: 0.8705 (pm20) REVERT: A 68 TRP cc_start: 0.9396 (m100) cc_final: 0.9038 (m100) REVERT: B 67 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.7632 (tpp) REVERT: B 272 ARG cc_start: 0.8611 (mtt90) cc_final: 0.8273 (ttm110) REVERT: E 59 ASP cc_start: 0.8595 (t0) cc_final: 0.8193 (t0) REVERT: E 110 GLN cc_start: 0.8645 (mp10) cc_final: 0.7806 (pp30) REVERT: F 79 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8752 (mm) REVERT: G 3 GLN cc_start: 0.8120 (mp10) cc_final: 0.7658 (mp10) REVERT: G 59 ASP cc_start: 0.9020 (t0) cc_final: 0.8518 (t0) outliers start: 14 outliers final: 7 residues processed: 72 average time/residue: 0.2070 time to fit residues: 21.9778 Evaluate side-chains 73 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9150 Z= 0.268 Angle : 0.645 11.911 12410 Z= 0.334 Chirality : 0.043 0.235 1330 Planarity : 0.003 0.029 1578 Dihedral : 4.823 41.142 1233 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.54 % Allowed : 14.37 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.34 (0.26), residues: 1122 helix: 0.49 (0.58), residues: 76 sheet: -0.69 (0.30), residues: 344 loop : -1.16 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 108 HIS 0.004 0.001 HIS B 195 PHE 0.026 0.001 PHE B 20 TYR 0.010 0.001 TYR H 87 ARG 0.004 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8705 (pm20) REVERT: A 68 TRP cc_start: 0.9400 (m100) cc_final: 0.9038 (m100) REVERT: B 67 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7383 (tpp) REVERT: B 123 MET cc_start: 0.8420 (tpt) cc_final: 0.7564 (tpp) REVERT: B 272 ARG cc_start: 0.8604 (mtt90) cc_final: 0.8283 (ttm110) REVERT: E 59 ASP cc_start: 0.8610 (t0) cc_final: 0.8185 (t0) REVERT: F 79 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8778 (mm) REVERT: G 59 ASP cc_start: 0.9006 (t0) cc_final: 0.8454 (t0) outliers start: 15 outliers final: 7 residues processed: 72 average time/residue: 0.2019 time to fit residues: 21.4277 Evaluate side-chains 72 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9150 Z= 0.171 Angle : 0.634 11.816 12410 Z= 0.325 Chirality : 0.043 0.234 1330 Planarity : 0.003 0.033 1578 Dihedral : 4.583 36.695 1233 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.03 % Allowed : 15.50 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.19 (0.26), residues: 1122 helix: 0.69 (0.60), residues: 72 sheet: -0.55 (0.31), residues: 318 loop : -1.08 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 108 HIS 0.002 0.001 HIS A 224 PHE 0.010 0.001 PHE A 34 TYR 0.009 0.001 TYR H 92 ARG 0.003 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8695 (pm20) REVERT: B 123 MET cc_start: 0.8391 (tpt) cc_final: 0.7505 (tpp) REVERT: B 272 ARG cc_start: 0.8557 (mtt90) cc_final: 0.8252 (ttm110) REVERT: E 59 ASP cc_start: 0.8411 (t0) cc_final: 0.8019 (t0) REVERT: E 110 GLN cc_start: 0.8511 (mp10) cc_final: 0.7732 (pp30) REVERT: F 79 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8710 (mm) REVERT: G 59 ASP cc_start: 0.9058 (t0) cc_final: 0.8526 (t0) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.2233 time to fit residues: 24.3048 Evaluate side-chains 75 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9150 Z= 0.187 Angle : 0.632 11.807 12410 Z= 0.323 Chirality : 0.043 0.233 1330 Planarity : 0.003 0.035 1578 Dihedral : 4.393 23.828 1230 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 1.44 % Allowed : 15.40 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.14 (0.26), residues: 1122 helix: 0.71 (0.61), residues: 72 sheet: -0.61 (0.30), residues: 344 loop : -0.99 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 108 HIS 0.004 0.001 HIS A 224 PHE 0.029 0.001 PHE B 20 TYR 0.008 0.001 TYR H 92 ARG 0.004 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8695 (pm20) REVERT: B 123 MET cc_start: 0.8404 (tpt) cc_final: 0.7563 (tpp) REVERT: B 174 ARG cc_start: 0.8799 (ptt-90) cc_final: 0.8048 (pmt-80) REVERT: B 272 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8241 (ttm110) REVERT: E 59 ASP cc_start: 0.8455 (t0) cc_final: 0.8055 (t0) REVERT: E 65 LYS cc_start: 0.9383 (mmmm) cc_final: 0.9142 (mmmm) REVERT: F 79 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8755 (mm) REVERT: G 59 ASP cc_start: 0.9061 (t0) cc_final: 0.8524 (t0) outliers start: 14 outliers final: 9 residues processed: 74 average time/residue: 0.2430 time to fit residues: 25.8116 Evaluate side-chains 76 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN B 255 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9150 Z= 0.412 Angle : 0.732 11.969 12410 Z= 0.375 Chirality : 0.045 0.236 1330 Planarity : 0.004 0.037 1578 Dihedral : 4.933 26.928 1230 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 1.33 % Allowed : 16.22 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.24 (0.26), residues: 1122 helix: 0.85 (0.62), residues: 72 sheet: -0.60 (0.30), residues: 328 loop : -1.12 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 168 HIS 0.006 0.001 HIS A 224 PHE 0.017 0.001 PHE A 34 TYR 0.015 0.002 TYR H 87 ARG 0.005 0.001 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 1.015 Fit side-chains REVERT: A 47 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8702 (pm20) REVERT: B 123 MET cc_start: 0.8638 (tpt) cc_final: 0.7900 (tpp) REVERT: B 272 ARG cc_start: 0.8680 (mtt90) cc_final: 0.8382 (ttm110) REVERT: E 59 ASP cc_start: 0.8906 (t0) cc_final: 0.8308 (t0) REVERT: E 100 TYR cc_start: 0.8077 (t80) cc_final: 0.7804 (t80) REVERT: E 110 GLN cc_start: 0.8521 (mp10) cc_final: 0.7735 (pp30) REVERT: F 79 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8808 (mm) REVERT: G 59 ASP cc_start: 0.9098 (t0) cc_final: 0.8867 (t0) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 0.2367 time to fit residues: 24.6756 Evaluate side-chains 72 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 6.9990 chunk 72 optimal weight: 0.0270 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.0020 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.6650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9150 Z= 0.175 Angle : 0.663 11.805 12410 Z= 0.338 Chirality : 0.044 0.236 1330 Planarity : 0.003 0.037 1578 Dihedral : 4.540 24.838 1230 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.13 % Allowed : 16.63 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.13 (0.26), residues: 1122 helix: 0.77 (0.62), residues: 72 sheet: -0.52 (0.31), residues: 318 loop : -1.02 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 108 HIS 0.003 0.001 HIS A 224 PHE 0.030 0.001 PHE B 20 TYR 0.008 0.001 TYR F 50 ARG 0.004 0.000 ARG B 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.979 Fit side-chains REVERT: A 47 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8694 (pm20) REVERT: B 123 MET cc_start: 0.8540 (tpt) cc_final: 0.7803 (tpp) REVERT: B 174 ARG cc_start: 0.8805 (ptt-90) cc_final: 0.8078 (pmt-80) REVERT: B 272 ARG cc_start: 0.8657 (mtt90) cc_final: 0.8377 (ttm110) REVERT: E 59 ASP cc_start: 0.8542 (t0) cc_final: 0.8081 (t0) REVERT: E 110 GLN cc_start: 0.8461 (mp10) cc_final: 0.7835 (pp30) REVERT: F 79 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8717 (mm) REVERT: G 59 ASP cc_start: 0.9090 (t0) cc_final: 0.8570 (t0) outliers start: 11 outliers final: 9 residues processed: 70 average time/residue: 0.2166 time to fit residues: 21.8893 Evaluate side-chains 74 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.2980 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 63 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.062849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.045809 restraints weight = 41346.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047279 restraints weight = 19983.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048307 restraints weight = 13259.471| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9150 Z= 0.174 Angle : 0.658 11.839 12410 Z= 0.334 Chirality : 0.043 0.232 1330 Planarity : 0.003 0.039 1578 Dihedral : 4.384 23.392 1230 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.03 % Allowed : 17.04 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.09 (0.26), residues: 1122 helix: 0.62 (0.61), residues: 72 sheet: -0.47 (0.30), residues: 338 loop : -1.00 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 108 HIS 0.003 0.000 HIS A 224 PHE 0.006 0.001 PHE A 34 TYR 0.008 0.001 TYR A 323 ARG 0.004 0.000 ARG B 174 =============================================================================== Job complete usr+sys time: 1751.36 seconds wall clock time: 33 minutes 12.12 seconds (1992.12 seconds total)