Starting phenix.real_space_refine on Thu Mar 13 15:30:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wur_32839/03_2025/7wur_32839.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wur_32839/03_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_32839/03_2025/7wur_32839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wur_32839/03_2025/7wur_32839.map" model { file = "/net/cci-nas-00/data/ceres_data/7wur_32839/03_2025/7wur_32839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wur_32839/03_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-5624/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: 6.66, per 1000 atoms: 0.75 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: 2.27 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: 1.26 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: 2.45 Time building geometry restraints manager: 2.74 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: 0.980 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.020 Find NCS groups from input model: 0.240 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.760 ------------------------------------------------------------------------------- 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 : 1.039 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: 0.2008 time to fit residues: 20.0898 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 : 1.182 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046489 restraints weight = 41494.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047976 restraints weight = 19861.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048998 restraints weight = 13078.981| |-----------------------------------------------------------------------------| 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 : 1.117 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: 0.8443 (mtt90) cc_final: 0.8180 (ttm110) outliers start: 8 outliers final: 3 residues processed: 73 average time/residue: 0.2137 time to fit residues: 22.5167 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 : 0.938 ------------------------------------------------------------------------------- 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: 8.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 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 = 0.3318 r_free = 0.3318 target = 0.059829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.042868 restraints weight = 43239.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.044330 restraints weight = 20646.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.045256 restraints weight = 13573.496| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 9150 Z= 0.542 Angle : 0.766 12.192 12410 Z= 0.400 Chirality : 0.045 0.235 1330 Planarity : 0.004 0.039 1578 Dihedral : 5.629 54.059 1234 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 1.33 % Allowed : 12.32 % 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: -1.53 (0.26), residues: 1122 helix: 0.09 (0.60), residues: 72 sheet: -0.82 (0.30), residues: 334 loop : -1.25 (0.24), residues: 716 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 0.016 0.002 PHE A 34 TYR 0.020 0.002 TYR H 87 ARG 0.005 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 78 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.9067 (pm20) cc_final: 0.8683 (pm20) REVERT: B 34 PHE cc_start: 0.6500 (m-80) cc_final: 0.6195 (m-80) REVERT: E 59 ASP cc_start: 0.8920 (t0) cc_final: 0.8455 (t0) REVERT: E 100 TYR cc_start: 0.8220 (t80) cc_final: 0.7854 (t80) REVERT: F 1 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8333 (tp30) REVERT: F 91 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8850 (tm-30) REVERT: G 3 GLN cc_start: 0.8126 (mp10) cc_final: 0.7850 (mp10) outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 0.1997 time to fit residues: 21.4543 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 : 1.037 ------------------------------------------------------------------------------- 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: 0.4980 chunk 106 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 87 optimal weight: 0.0770 chunk 91 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.062448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.045642 restraints weight = 41197.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047142 restraints weight = 19346.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048164 restraints weight = 12605.075| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9150 Z= 0.166 Angle : 0.626 11.883 12410 Z= 0.327 Chirality : 0.043 0.239 1330 Planarity : 0.003 0.032 1578 Dihedral : 4.944 50.837 1233 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.72 % Allowed : 13.96 % Favored : 85.32 % 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: -1.40 (0.26), residues: 1122 helix: 0.24 (0.59), residues: 72 sheet: -0.46 (0.30), residues: 318 loop : -1.31 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 108 HIS 0.002 0.001 HIS B 195 PHE 0.032 0.001 PHE A 34 TYR 0.009 0.001 TYR H 92 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: 7 poor density : 68 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.9001 (pm20) cc_final: 0.8692 (pm20) REVERT: A 67 MET cc_start: 0.8585 (tpp) cc_final: 0.8328 (tpp) REVERT: A 184 MET cc_start: 0.8613 (tpp) cc_final: 0.8220 (ttt) REVERT: B 67 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7703 (tpp) REVERT: B 123 MET cc_start: 0.8338 (tpt) cc_final: 0.7341 (tpp) REVERT: E 59 ASP cc_start: 0.8387 (t0) cc_final: 0.8033 (t0) REVERT: E 76 LYS cc_start: 0.9508 (ptpp) cc_final: 0.9290 (ptpp) REVERT: G 3 GLN cc_start: 0.8019 (mp10) cc_final: 0.7808 (mp10) outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.2028 time to fit residues: 21.1087 Evaluate side-chains 70 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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: 0.0060 chunk 5 optimal weight: 0.0370 chunk 16 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 78 optimal weight: 0.0040 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.8090 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.062543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.045537 restraints weight = 41436.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.047054 restraints weight = 19637.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.048078 restraints weight = 12875.016| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1870 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= 0.174 Angle : 0.619 11.832 12410 Z= 0.320 Chirality : 0.043 0.236 1330 Planarity : 0.003 0.036 1578 Dihedral : 4.698 44.988 1233 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.54 % Allowed : 14.89 % Favored : 83.57 % 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: -1.28 (0.26), residues: 1122 helix: 0.20 (0.58), residues: 72 sheet: -0.49 (0.30), residues: 330 loop : -1.15 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 108 HIS 0.002 0.001 HIS B 195 PHE 0.009 0.001 PHE A 34 TYR 0.012 0.001 TYR A 32 ARG 0.009 0.000 ARG B 174 *********************** 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 79 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.945 Fit side-chains REVERT: A 47 GLN cc_start: 0.8991 (pm20) cc_final: 0.8719 (pm20) REVERT: A 67 MET cc_start: 0.8373 (tpp) cc_final: 0.8123 (tpp) REVERT: A 97 MET cc_start: 0.8777 (mmt) cc_final: 0.8404 (tpp) REVERT: A 184 MET cc_start: 0.8448 (tpp) cc_final: 0.7923 (ttt) REVERT: B 67 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7559 (tpp) REVERT: B 123 MET cc_start: 0.8172 (tpt) cc_final: 0.7178 (tpp) REVERT: E 59 ASP cc_start: 0.8353 (t0) cc_final: 0.7982 (t0) REVERT: E 76 LYS cc_start: 0.9503 (ptpp) cc_final: 0.9274 (ptpp) REVERT: F 79 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8713 (mm) REVERT: G 3 GLN cc_start: 0.7994 (mp10) cc_final: 0.7579 (mp10) REVERT: G 59 ASP cc_start: 0.8941 (t0) cc_final: 0.8462 (t0) outliers start: 15 outliers final: 5 residues processed: 75 average time/residue: 0.2099 time to fit residues: 22.9455 Evaluate side-chains 69 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 70 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 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 ** 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 = 0.3392 r_free = 0.3392 target = 0.062337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.045334 restraints weight = 41462.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.046802 restraints weight = 19856.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.047805 restraints weight = 13109.171| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2037 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= 0.207 Angle : 0.632 11.821 12410 Z= 0.326 Chirality : 0.043 0.236 1330 Planarity : 0.003 0.035 1578 Dihedral : 4.698 42.673 1233 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.44 % Allowed : 16.02 % Favored : 82.55 % 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: -1.26 (0.26), residues: 1122 helix: 0.39 (0.60), residues: 72 sheet: -0.66 (0.29), residues: 342 loop : -1.06 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 108 HIS 0.003 0.001 HIS B 195 PHE 0.026 0.001 PHE B 20 TYR 0.013 0.001 TYR A 32 ARG 0.004 0.000 ARG B 174 *********************** 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 77 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 1.615 Fit side-chains REVERT: A 47 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8673 (pm20) REVERT: A 184 MET cc_start: 0.8504 (tpp) cc_final: 0.8054 (ttt) REVERT: B 67 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.7502 (tpp) REVERT: B 123 MET cc_start: 0.8255 (tpt) cc_final: 0.7300 (tpp) REVERT: E 59 ASP cc_start: 0.8421 (t0) cc_final: 0.8012 (t0) REVERT: E 110 GLN cc_start: 0.8464 (mp10) cc_final: 0.7724 (pp30) REVERT: F 79 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8812 (mm) REVERT: G 59 ASP cc_start: 0.8968 (t0) cc_final: 0.8393 (t0) outliers start: 14 outliers final: 7 residues processed: 71 average time/residue: 0.1973 time to fit residues: 20.7089 Evaluate side-chains 71 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 74 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.062171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.045183 restraints weight = 41932.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.046673 restraints weight = 19778.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.047653 restraints weight = 12958.871| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2175 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= 0.205 Angle : 0.630 11.833 12410 Z= 0.325 Chirality : 0.043 0.235 1330 Planarity : 0.003 0.034 1578 Dihedral : 4.655 40.674 1233 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % 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: -1.20 (0.26), residues: 1122 helix: 0.54 (0.60), residues: 72 sheet: -0.57 (0.30), residues: 338 loop : -1.06 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 108 HIS 0.003 0.001 HIS B 195 PHE 0.006 0.001 PHE A 217 TYR 0.011 0.001 TYR A 32 ARG 0.004 0.000 ARG B 174 *********************** 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 76 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.065 Fit side-chains REVERT: A 47 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8683 (pm20) REVERT: A 67 MET cc_start: 0.7973 (tpp) cc_final: 0.7760 (tpt) REVERT: A 184 MET cc_start: 0.8464 (tpp) cc_final: 0.8066 (ttt) REVERT: B 123 MET cc_start: 0.8344 (tpt) cc_final: 0.7452 (tpp) REVERT: E 59 ASP cc_start: 0.8473 (t0) cc_final: 0.8044 (t0) REVERT: E 65 LYS cc_start: 0.9423 (mmmm) cc_final: 0.9166 (mmmm) REVERT: E 76 LYS cc_start: 0.9494 (ptpp) cc_final: 0.9294 (ptpp) REVERT: F 79 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8820 (mm) REVERT: G 59 ASP cc_start: 0.9017 (t0) cc_final: 0.8427 (t0) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.2102 time to fit residues: 22.2265 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 : 1.120 ------------------------------------------------------------------------------- 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 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 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 54 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 81 optimal weight: 0.0670 chunk 21 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.061450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.044398 restraints weight = 42310.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.045879 restraints weight = 20174.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046858 restraints weight = 13302.037| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9150 Z= 0.269 Angle : 0.658 11.872 12410 Z= 0.338 Chirality : 0.043 0.236 1330 Planarity : 0.003 0.034 1578 Dihedral : 4.578 25.111 1230 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % 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: -1.19 (0.26), residues: 1122 helix: 0.58 (0.60), residues: 72 sheet: -0.61 (0.30), residues: 342 loop : -1.04 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 108 HIS 0.004 0.001 HIS B 195 PHE 0.028 0.001 PHE B 20 TYR 0.012 0.001 TYR A 323 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: 15 poor density : 64 time to evaluate : 1.519 Fit side-chains REVERT: A 47 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8655 (pm20) REVERT: A 184 MET cc_start: 0.8445 (tpp) cc_final: 0.8092 (ttt) REVERT: B 67 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7299 (tpp) REVERT: B 123 MET cc_start: 0.8432 (tpt) cc_final: 0.7585 (tpp) REVERT: E 58 THR cc_start: 0.9205 (p) cc_final: 0.9003 (t) REVERT: E 59 ASP cc_start: 0.8612 (t0) cc_final: 0.8110 (t0) REVERT: E 65 LYS cc_start: 0.9434 (mmmm) cc_final: 0.9169 (mmmm) REVERT: E 76 LYS cc_start: 0.9491 (ptpp) cc_final: 0.9285 (ptpp) REVERT: E 110 GLN cc_start: 0.8525 (mp10) cc_final: 0.7782 (pp30) REVERT: F 79 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8825 (mm) REVERT: G 59 ASP cc_start: 0.9055 (t0) cc_final: 0.8450 (t0) outliers start: 15 outliers final: 9 residues processed: 72 average time/residue: 0.2107 time to fit residues: 22.0997 Evaluate side-chains 74 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.062452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.045461 restraints weight = 41467.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.046980 restraints weight = 19756.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047978 restraints weight = 12974.574| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9150 Z= 0.180 Angle : 0.646 11.802 12410 Z= 0.330 Chirality : 0.043 0.234 1330 Planarity : 0.003 0.036 1578 Dihedral : 4.380 24.096 1230 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.13 % Allowed : 16.94 % 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: -1.15 (0.26), residues: 1122 helix: 0.55 (0.59), residues: 72 sheet: -0.57 (0.30), residues: 342 loop : -1.00 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 108 HIS 0.002 0.001 HIS B 195 PHE 0.015 0.001 PHE A 34 TYR 0.008 0.001 TYR H 92 ARG 0.004 0.000 ARG B 174 *********************** 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 79 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 1.047 Fit side-chains REVERT: A 47 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8649 (pm20) REVERT: B 67 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.7502 (tpp) REVERT: B 123 MET cc_start: 0.8363 (tpt) cc_final: 0.7582 (tpp) REVERT: B 174 ARG cc_start: 0.8713 (ptt-90) cc_final: 0.8016 (pmt-80) REVERT: E 59 ASP cc_start: 0.8434 (t0) cc_final: 0.8009 (t0) REVERT: E 65 LYS cc_start: 0.9411 (mmmm) cc_final: 0.9143 (mmmm) REVERT: E 110 GLN cc_start: 0.8461 (mp10) cc_final: 0.7765 (pp30) REVERT: F 79 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8822 (mm) REVERT: G 59 ASP cc_start: 0.9011 (t0) cc_final: 0.8437 (t0) outliers start: 11 outliers final: 6 residues processed: 75 average time/residue: 0.2151 time to fit residues: 23.2491 Evaluate side-chains 72 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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: 2.9990 chunk 109 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 0.0570 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 28 optimal weight: 0.0170 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.063227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.046274 restraints weight = 41620.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.047796 restraints weight = 19911.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.048803 restraints weight = 13118.704| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2405 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= 0.163 Angle : 0.657 11.884 12410 Z= 0.333 Chirality : 0.044 0.235 1330 Planarity : 0.003 0.036 1578 Dihedral : 4.226 22.888 1230 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.13 % Allowed : 17.15 % 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: -1.13 (0.26), residues: 1122 helix: 0.57 (0.60), residues: 72 sheet: -0.48 (0.29), residues: 350 loop : -1.04 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 108 HIS 0.002 0.000 HIS A 26 PHE 0.030 0.001 PHE B 20 TYR 0.010 0.001 TYR A 32 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 81 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8625 (pm20) REVERT: A 101 LYS cc_start: 0.9128 (mmpt) cc_final: 0.8743 (mmmt) REVERT: A 184 MET cc_start: 0.8352 (ttm) cc_final: 0.7856 (ttt) REVERT: B 67 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.7323 (tpp) REVERT: B 123 MET cc_start: 0.8353 (tpt) cc_final: 0.7574 (tpp) REVERT: B 174 ARG cc_start: 0.8702 (ptt-90) cc_final: 0.8138 (pmt-80) REVERT: E 59 ASP cc_start: 0.8350 (t0) cc_final: 0.7964 (t0) REVERT: E 65 LYS cc_start: 0.9404 (mmmm) cc_final: 0.9145 (mmmm) REVERT: E 110 GLN cc_start: 0.8412 (mp10) cc_final: 0.7815 (pp30) REVERT: F 79 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8815 (mm) REVERT: G 59 ASP cc_start: 0.8999 (t0) cc_final: 0.8423 (t0) outliers start: 11 outliers final: 5 residues processed: 77 average time/residue: 0.2149 time to fit residues: 23.5623 Evaluate side-chains 74 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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: 0.0870 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.062479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.045431 restraints weight = 41889.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.046941 restraints weight = 20097.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.047916 restraints weight = 13267.448| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9150 Z= 0.203 Angle : 0.662 12.016 12410 Z= 0.335 Chirality : 0.044 0.233 1330 Planarity : 0.003 0.037 1578 Dihedral : 4.308 23.531 1230 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.82 % Allowed : 17.76 % Favored : 81.42 % 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: -0.98 (0.26), residues: 1122 helix: 1.03 (0.62), residues: 68 sheet: -0.43 (0.30), residues: 326 loop : -0.92 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 68 HIS 0.003 0.001 HIS B 195 PHE 0.022 0.001 PHE A 34 TYR 0.016 0.001 TYR A 32 ARG 0.006 0.000 ARG F 18 =============================================================================== Job complete usr+sys time: 2913.33 seconds wall clock time: 53 minutes 12.72 seconds (3192.72 seconds total)