Starting phenix.real_space_refine on Thu Feb 13 12:57:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wur_32839/02_2025/7wur_32839.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wur_32839/02_2025/7wur_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_32839/02_2025/7wur_32839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wur_32839/02_2025/7wur_32839.map" model { file = "/net/cci-nas-00/data/ceres_data/7wur_32839/02_2025/7wur_32839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wur_32839/02_2025/7wur_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-5592/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: 5.40, per 1000 atoms: 0.61 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: 2.24 Conformation dependent library (CDL) restraints added in 1.0 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: 1.11 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: 2.55 Time building geometry restraints manager: 2.64 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: 0.01 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 22.920 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.780 ------------------------------------------------------------------------------- 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 : 0.999 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: 0.2086 time to fit residues: 20.7696 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 : 1.023 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.063373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046497 restraints weight = 41494.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047971 restraints weight = 19860.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048993 restraints weight = 13089.666| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.858 Fit side-chains revert: symmetry clash REVERT: B 174 ARG cc_start: 0.8554 (ptp90) cc_final: 0.8097 (pmt-80) REVERT: B 272 ARG cc_start: 0.8444 (mtt90) cc_final: 0.8180 (ttm110) outliers start: 8 outliers final: 3 residues processed: 73 average time/residue: 0.2173 time to fit residues: 22.8103 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 : 1.082 ------------------------------------------------------------------------------- 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 64 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.059804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.042837 restraints weight = 43312.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.044287 restraints weight = 20728.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.045217 restraints weight = 13662.076| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 9150 Z= 0.571 Angle : 0.774 12.192 12410 Z= 0.404 Chirality : 0.045 0.237 1330 Planarity : 0.004 0.039 1578 Dihedral : 5.574 52.729 1234 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 1.23 % Allowed : 12.42 % Favored : 86.34 % 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: -1.57 (0.26), residues: 1122 helix: 0.01 (0.59), residues: 72 sheet: -0.92 (0.29), residues: 344 loop : -1.23 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 168 HIS 0.007 0.001 HIS B 195 PHE 0.018 0.002 PHE B 34 TYR 0.021 0.002 TYR H 87 ARG 0.006 0.001 ARG E 72 *********************** 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 77 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.9075 (pm20) cc_final: 0.8692 (pm20) REVERT: B 34 PHE cc_start: 0.6396 (m-80) cc_final: 0.6089 (m-10) REVERT: E 59 ASP cc_start: 0.8886 (t0) cc_final: 0.8428 (t0) REVERT: E 100 TYR cc_start: 0.8226 (t80) cc_final: 0.7902 (t80) REVERT: F 1 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8383 (tp30) REVERT: F 91 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8887 (tm-30) REVERT: G 3 GLN cc_start: 0.8128 (mp10) cc_final: 0.7836 (mp10) REVERT: H 102 GLN cc_start: 0.9245 (mm-40) cc_final: 0.9040 (mm-40) outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 0.2024 time to fit residues: 21.3070 Evaluate side-chains 70 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 B residue 139 GLU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain F residue 91 GLN 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 107 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.061470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.044569 restraints weight = 41729.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.046027 restraints weight = 19835.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.047021 restraints weight = 13053.590| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9150 Z= 0.222 Angle : 0.640 11.942 12410 Z= 0.335 Chirality : 0.043 0.240 1330 Planarity : 0.004 0.033 1578 Dihedral : 5.146 54.356 1233 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.92 % Allowed : 14.17 % Favored : 84.91 % 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: -1.45 (0.26), residues: 1122 helix: 0.26 (0.59), residues: 72 sheet: -0.59 (0.30), residues: 334 loop : -1.30 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 108 HIS 0.003 0.001 HIS B 195 PHE 0.028 0.001 PHE A 34 TYR 0.010 0.001 TYR A 32 ARG 0.004 0.000 ARG B 272 *********************** 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 75 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.9032 (pm20) cc_final: 0.8630 (pm20) REVERT: A 67 MET cc_start: 0.8550 (tpp) cc_final: 0.8158 (tpp) REVERT: A 184 MET cc_start: 0.8641 (tpp) cc_final: 0.8296 (ttt) REVERT: B 67 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.7792 (tpp) REVERT: B 123 MET cc_start: 0.8291 (tpt) cc_final: 0.7263 (tpp) REVERT: E 58 THR cc_start: 0.9237 (p) cc_final: 0.8964 (t) REVERT: E 59 ASP cc_start: 0.8488 (t0) cc_final: 0.8056 (t0) REVERT: E 76 LYS cc_start: 0.9494 (ptpp) cc_final: 0.9268 (ptpp) REVERT: G 3 GLN cc_start: 0.8033 (mp10) cc_final: 0.7805 (mp10) REVERT: G 59 ASP cc_start: 0.9036 (t0) cc_final: 0.8812 (t0) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.2021 time to fit residues: 21.2845 Evaluate side-chains 70 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 B residue 236 VAL Chi-restraints excluded: chain F residue 3 VAL 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 58 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.062012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.045054 restraints weight = 41542.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046557 restraints weight = 19789.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.047572 restraints weight = 12955.375| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9150 Z= 0.198 Angle : 0.626 11.897 12410 Z= 0.325 Chirality : 0.043 0.237 1330 Planarity : 0.003 0.034 1578 Dihedral : 4.859 45.855 1233 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.44 % Allowed : 14.89 % Favored : 83.68 % 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: -1.33 (0.26), residues: 1122 helix: 0.31 (0.59), residues: 72 sheet: -0.54 (0.31), residues: 318 loop : -1.20 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 108 HIS 0.002 0.001 HIS B 195 PHE 0.010 0.001 PHE A 34 TYR 0.012 0.001 TYR A 32 ARG 0.003 0.000 ARG B 272 *********************** 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 : 1.015 Fit side-chains REVERT: A 47 GLN cc_start: 0.9008 (pm20) cc_final: 0.8727 (pm20) REVERT: A 97 MET cc_start: 0.8775 (mmt) cc_final: 0.8388 (tpp) REVERT: A 184 MET cc_start: 0.8472 (tpp) cc_final: 0.7979 (ttt) REVERT: B 67 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.7576 (tpp) REVERT: B 123 MET cc_start: 0.8361 (tpt) cc_final: 0.7430 (tpp) REVERT: E 59 ASP cc_start: 0.8504 (t0) cc_final: 0.8101 (t0) REVERT: E 76 LYS cc_start: 0.9519 (ptpp) cc_final: 0.9297 (ptpp) REVERT: E 110 GLN cc_start: 0.8445 (mp10) cc_final: 0.7655 (pp30) REVERT: F 79 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8709 (mm) REVERT: G 3 GLN cc_start: 0.8025 (mp10) cc_final: 0.7806 (mp10) REVERT: G 59 ASP cc_start: 0.9001 (t0) cc_final: 0.8393 (t0) outliers start: 14 outliers final: 7 residues processed: 74 average time/residue: 0.1867 time to fit residues: 20.9597 Evaluate side-chains 69 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 0.0030 chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.060680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.043705 restraints weight = 41982.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.045164 restraints weight = 20197.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.046118 restraints weight = 13319.258| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9150 Z= 0.347 Angle : 0.684 11.950 12410 Z= 0.353 Chirality : 0.044 0.239 1330 Planarity : 0.004 0.035 1578 Dihedral : 5.089 44.677 1233 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 1.85 % Allowed : 16.22 % 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: -1.33 (0.26), residues: 1122 helix: 0.52 (0.60), residues: 72 sheet: -0.54 (0.31), residues: 318 loop : -1.22 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 108 HIS 0.005 0.001 HIS B 195 PHE 0.027 0.001 PHE B 20 TYR 0.013 0.001 TYR H 87 ARG 0.004 0.000 ARG E 72 *********************** 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: 18 poor density : 61 time to evaluate : 1.024 Fit side-chains REVERT: A 47 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8703 (pm20) REVERT: A 262 THR cc_start: 0.9616 (OUTLIER) cc_final: 0.9396 (m) REVERT: B 47 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: B 67 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7480 (tpp) REVERT: B 123 MET cc_start: 0.8463 (tpt) cc_final: 0.7600 (tpp) REVERT: B 241 MET cc_start: 0.8859 (mtp) cc_final: 0.8620 (mtt) REVERT: E 59 ASP cc_start: 0.8775 (t0) cc_final: 0.8246 (t0) REVERT: F 79 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8834 (mm) REVERT: F 91 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8885 (tm-30) REVERT: G 59 ASP cc_start: 0.9037 (t0) cc_final: 0.8810 (t0) outliers start: 18 outliers final: 8 residues processed: 74 average time/residue: 0.1781 time to fit residues: 20.0243 Evaluate side-chains 72 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain B residue 47 GLN 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 E residue 114 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 114 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 83 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.060730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.043758 restraints weight = 42384.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.045212 restraints weight = 20146.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.046176 restraints weight = 13278.863| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9150 Z= 0.314 Angle : 0.688 11.938 12410 Z= 0.353 Chirality : 0.044 0.241 1330 Planarity : 0.004 0.035 1578 Dihedral : 5.052 43.274 1233 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.85 % Allowed : 16.22 % 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: -1.30 (0.26), residues: 1122 helix: 0.58 (0.60), residues: 72 sheet: -0.55 (0.30), residues: 322 loop : -1.19 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 108 HIS 0.005 0.001 HIS A 224 PHE 0.008 0.001 PHE A 279 TYR 0.011 0.001 TYR A 32 ARG 0.003 0.000 ARG E 72 *********************** 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 79 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 1.097 Fit side-chains REVERT: A 47 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8697 (pm20) REVERT: A 184 MET cc_start: 0.8685 (ttm) cc_final: 0.8252 (ttt) REVERT: A 262 THR cc_start: 0.9628 (OUTLIER) cc_final: 0.9409 (m) REVERT: B 47 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: B 67 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.7331 (tpp) REVERT: B 123 MET cc_start: 0.8515 (tpt) cc_final: 0.7727 (tpp) REVERT: E 59 ASP cc_start: 0.8726 (t0) cc_final: 0.8256 (t0) REVERT: E 110 GLN cc_start: 0.8667 (mp10) cc_final: 0.7740 (pp30) REVERT: F 79 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8840 (mm) REVERT: F 91 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8874 (tm-30) REVERT: G 59 ASP cc_start: 0.9058 (t0) cc_final: 0.8551 (t0) outliers start: 18 outliers final: 8 residues processed: 73 average time/residue: 0.2057 time to fit residues: 22.1637 Evaluate side-chains 72 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain B residue 47 GLN 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 E residue 114 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 114 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 54 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 83 optimal weight: 0.0060 chunk 81 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.060868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.043868 restraints weight = 42544.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.045352 restraints weight = 20317.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.046323 restraints weight = 13399.891| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9150 Z= 0.280 Angle : 0.682 11.930 12410 Z= 0.350 Chirality : 0.044 0.239 1330 Planarity : 0.004 0.036 1578 Dihedral : 4.995 42.128 1233 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.54 % Allowed : 16.74 % Favored : 81.72 % 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: -1.30 (0.26), residues: 1122 helix: 0.61 (0.60), residues: 72 sheet: -0.69 (0.30), residues: 330 loop : -1.11 (0.25), residues: 720 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 0.028 0.001 PHE B 20 TYR 0.013 0.001 TYR A 32 ARG 0.002 0.000 ARG E 72 *********************** 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 76 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.978 Fit side-chains REVERT: A 47 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8692 (pm20) REVERT: A 262 THR cc_start: 0.9616 (OUTLIER) cc_final: 0.9397 (m) REVERT: B 47 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: B 67 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.7302 (tpp) REVERT: B 123 MET cc_start: 0.8624 (tpt) cc_final: 0.7892 (tpp) REVERT: E 59 ASP cc_start: 0.8802 (t0) cc_final: 0.8394 (t0) REVERT: E 65 LYS cc_start: 0.9451 (mmmm) cc_final: 0.9187 (mmmm) REVERT: E 110 GLN cc_start: 0.8603 (mp10) cc_final: 0.7852 (pp30) REVERT: F 79 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8837 (mm) REVERT: F 91 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8927 (tm-30) REVERT: G 59 ASP cc_start: 0.9059 (t0) cc_final: 0.8555 (t0) outliers start: 15 outliers final: 9 residues processed: 71 average time/residue: 0.1992 time to fit residues: 20.9155 Evaluate side-chains 75 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain B residue 47 GLN 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 E residue 114 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 114 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 33 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.062313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.045305 restraints weight = 41744.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.046780 restraints weight = 20036.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047774 restraints weight = 13289.399| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9150 Z= 0.178 Angle : 0.657 12.605 12410 Z= 0.335 Chirality : 0.043 0.237 1330 Planarity : 0.003 0.039 1578 Dihedral : 4.679 39.420 1233 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.13 % Allowed : 17.25 % Favored : 81.62 % 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: 0.91 (0.61), residues: 68 sheet: -0.58 (0.30), residues: 328 loop : -0.96 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 68 HIS 0.002 0.001 HIS A 26 PHE 0.020 0.001 PHE A 34 TYR 0.016 0.001 TYR A 32 ARG 0.002 0.000 ARG B 272 *********************** 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 77 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.067 Fit side-chains REVERT: A 47 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8676 (pm20) REVERT: B 47 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8370 (pp30) REVERT: B 123 MET cc_start: 0.8614 (tpt) cc_final: 0.7941 (tpp) REVERT: E 59 ASP cc_start: 0.8673 (t0) cc_final: 0.8241 (t0) REVERT: E 65 LYS cc_start: 0.9420 (mmmm) cc_final: 0.9146 (mmmm) REVERT: E 110 GLN cc_start: 0.8525 (mp10) cc_final: 0.7826 (pp30) REVERT: F 79 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8814 (mm) REVERT: G 59 ASP cc_start: 0.9020 (t0) cc_final: 0.8512 (t0) outliers start: 11 outliers final: 6 residues processed: 74 average time/residue: 0.1976 time to fit residues: 21.6432 Evaluate side-chains 71 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 97 MET 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 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 80 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 62 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.063071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.046138 restraints weight = 41723.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047643 restraints weight = 20116.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.048627 restraints weight = 13278.914| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9150 Z= 0.165 Angle : 0.672 16.920 12410 Z= 0.336 Chirality : 0.044 0.236 1330 Planarity : 0.003 0.038 1578 Dihedral : 4.315 26.565 1230 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.82 % Allowed : 18.07 % Favored : 81.11 % 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: -1.05 (0.26), residues: 1122 helix: 0.77 (0.63), residues: 68 sheet: -0.42 (0.30), residues: 338 loop : -0.99 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 68 HIS 0.002 0.000 HIS A 26 PHE 0.029 0.001 PHE B 20 TYR 0.023 0.001 TYR A 32 ARG 0.002 0.000 ARG B 272 ********************** 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 77 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: A 101 LYS cc_start: 0.9141 (mmpt) cc_final: 0.8737 (mmmt) REVERT: A 275 MET cc_start: 0.9195 (ttp) cc_final: 0.8975 (ttp) REVERT: B 47 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: B 123 MET cc_start: 0.8589 (tpt) cc_final: 0.7858 (tpp) REVERT: E 59 ASP cc_start: 0.8599 (t0) cc_final: 0.8204 (t0) REVERT: E 65 LYS cc_start: 0.9410 (mmmm) cc_final: 0.9151 (mmmm) REVERT: E 110 GLN cc_start: 0.8463 (mp10) cc_final: 0.7744 (pp30) REVERT: F 61 ASP cc_start: 0.8666 (p0) cc_final: 0.8461 (t0) REVERT: F 79 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8795 (mm) REVERT: G 59 ASP cc_start: 0.9039 (t0) cc_final: 0.8543 (t0) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 0.2004 time to fit residues: 21.9337 Evaluate side-chains 75 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 114 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 5 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 81 optimal weight: 0.0010 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.062326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.045361 restraints weight = 42169.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.046850 restraints weight = 20423.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.047815 restraints weight = 13565.614| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9150 Z= 0.203 Angle : 0.670 16.300 12410 Z= 0.337 Chirality : 0.044 0.237 1330 Planarity : 0.003 0.039 1578 Dihedral : 4.364 25.088 1230 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.92 % Allowed : 18.07 % Favored : 81.01 % 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: -1.01 (0.26), residues: 1122 helix: 0.83 (0.63), residues: 68 sheet: -0.43 (0.30), residues: 324 loop : -0.94 (0.25), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 68 HIS 0.003 0.001 HIS B 195 PHE 0.023 0.001 PHE A 34 TYR 0.013 0.001 TYR A 32 ARG 0.002 0.000 ARG E 72 =============================================================================== Job complete usr+sys time: 2665.62 seconds wall clock time: 48 minutes 57.49 seconds (2937.49 seconds total)