Starting phenix.real_space_refine on Thu Mar 13 09:10:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydh_33747/03_2025/7ydh_33747_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydh_33747/03_2025/7ydh_33747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ydh_33747/03_2025/7ydh_33747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydh_33747/03_2025/7ydh_33747.map" model { file = "/net/cci-nas-00/data/ceres_data/7ydh_33747/03_2025/7ydh_33747_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydh_33747/03_2025/7ydh_33747_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5589 2.51 5 N 1497 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8764 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1779 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 3, 'TRANS': 211} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2167 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 268} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 5.32, per 1000 atoms: 0.61 Number of scatterers: 8764 At special positions: 0 Unit cell: (93.5, 119.9, 133.1, 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 58 16.00 O 1620 8.00 N 1497 7.00 C 5589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.05 Simple disulfide: pdb=" SG CYS R 612 " - pdb=" SG CYS R 684 " 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: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 36.5% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 8 through 25 Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.714A pdb=" N LEU A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 removed outlier: 4.335A pdb=" N ASN A 136 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 137 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.560A pdb=" N ASP A 160 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A 161 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.723A pdb=" N VAL A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 228 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.602A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.680A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.683A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.060A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.625A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.709A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.521A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 55 through 59' Processing helix chain 'R' and resid 544 through 572 removed outlier: 3.517A pdb=" N THR R 548 " --> pdb=" O ASP R 544 " (cutoff:3.500A) Processing helix chain 'R' and resid 577 through 601 Processing helix chain 'R' and resid 609 through 642 removed outlier: 3.761A pdb=" N ARG R 613 " --> pdb=" O GLY R 609 " (cutoff:3.500A) Processing helix chain 'R' and resid 651 through 674 removed outlier: 3.802A pdb=" N VAL R 662 " --> pdb=" O ILE R 658 " (cutoff:3.500A) Proline residue: R 663 - end of helix Processing helix chain 'R' and resid 688 through 692 Processing helix chain 'R' and resid 693 through 720 removed outlier: 3.604A pdb=" N LEU R 697 " --> pdb=" O LEU R 693 " (cutoff:3.500A) Proline residue: R 699 - end of helix removed outlier: 3.568A pdb=" N PHE R 702 " --> pdb=" O GLY R 698 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS R 706 " --> pdb=" O PHE R 702 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL R 709 " --> pdb=" O LEU R 705 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL R 712 " --> pdb=" O ALA R 708 " (cutoff:3.500A) Processing helix chain 'R' and resid 721 through 726 Processing helix chain 'R' and resid 730 through 747 removed outlier: 3.700A pdb=" N THR R 741 " --> pdb=" O ALA R 737 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA R 742 " --> pdb=" O LEU R 738 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE R 743 " --> pdb=" O THR R 739 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 744 " --> pdb=" O ILE R 740 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE R 747 " --> pdb=" O ILE R 743 " (cutoff:3.500A) Processing helix chain 'R' and resid 750 through 759 removed outlier: 3.750A pdb=" N TRP R 753 " --> pdb=" O GLY R 750 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL R 754 " --> pdb=" O CYS R 751 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE R 755 " --> pdb=" O THR R 752 " (cutoff:3.500A) Processing helix chain 'R' and resid 765 through 777 removed outlier: 3.994A pdb=" N LEU R 777 " --> pdb=" O ILE R 773 " (cutoff:3.500A) Processing helix chain 'R' and resid 777 through 787 Processing helix chain 'R' and resid 790 through 804 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76 removed outlier: 4.219A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 105 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 143 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR A 200 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.097A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.395A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.881A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.093A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.657A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.617A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.712A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.122A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 142 through 143 Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.117A pdb=" N VAL E 148 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1098 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: 2.38 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2838 1.34 - 1.47: 2187 1.47 - 1.59: 3841 1.59 - 1.71: 0 1.71 - 1.84: 79 Bond restraints: 8945 Sorted by residual: bond pdb=" N TYR E 236 " pdb=" CA TYR E 236 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.14e-02 7.69e+03 9.18e+00 bond pdb=" N VAL R 644 " pdb=" CA VAL R 644 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.08e+00 bond pdb=" N ILE R 740 " pdb=" CA ILE R 740 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.28e-02 6.10e+03 7.77e+00 bond pdb=" N VAL R 642 " pdb=" CA VAL R 642 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.61e+00 bond pdb=" N MET R 537 " pdb=" CA MET R 537 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.16e-02 7.43e+03 7.07e+00 ... (remaining 8940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 11579 1.73 - 3.46: 453 3.46 - 5.19: 57 5.19 - 6.92: 12 6.92 - 8.64: 10 Bond angle restraints: 12111 Sorted by residual: angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 111.71 120.24 -8.53 1.34e+00 5.57e-01 4.05e+01 angle pdb=" N GLN A 191 " pdb=" CA GLN A 191 " pdb=" C GLN A 191 " ideal model delta sigma weight residual 108.13 115.64 -7.51 1.72e+00 3.38e-01 1.91e+01 angle pdb=" N ASP A 189 " pdb=" CA ASP A 189 " pdb=" C ASP A 189 " ideal model delta sigma weight residual 110.80 102.16 8.64 2.13e+00 2.20e-01 1.65e+01 angle pdb=" C TYR E 236 " pdb=" CA TYR E 236 " pdb=" CB TYR E 236 " ideal model delta sigma weight residual 109.56 116.19 -6.63 1.64e+00 3.72e-01 1.63e+01 angle pdb=" C ASN A 144 " pdb=" N LYS A 145 " pdb=" CA LYS A 145 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.37e+01 ... (remaining 12106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4938 17.71 - 35.42: 274 35.42 - 53.12: 60 53.12 - 70.83: 11 70.83 - 88.54: 4 Dihedral angle restraints: 5287 sinusoidal: 2065 harmonic: 3222 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 143.16 -50.16 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CA LYS A 145 " pdb=" C LYS A 145 " pdb=" N THR A 146 " pdb=" CA THR A 146 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CB CYS R 612 " pdb=" SG CYS R 612 " pdb=" SG CYS R 684 " pdb=" CB CYS R 684 " ideal model delta sinusoidal sigma weight residual -86.00 -119.89 33.89 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 5284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1180 0.069 - 0.137: 169 0.137 - 0.206: 22 0.206 - 0.275: 3 0.275 - 0.344: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CA ALA B 203 " pdb=" N ALA B 203 " pdb=" C ALA B 203 " pdb=" CB ALA B 203 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA LYS A 145 " pdb=" N LYS A 145 " pdb=" C LYS A 145 " pdb=" CB LYS A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA ASP B 291 " pdb=" N ASP B 291 " pdb=" C ASP B 291 " pdb=" CB ASP B 291 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1373 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.062 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO B 39 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 783 " 0.006 2.00e-02 2.50e+03 1.65e-02 5.47e+00 pdb=" CG TYR R 783 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR R 783 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR R 783 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR R 783 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR R 783 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR R 783 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 783 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 731 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C LYS R 731 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS R 731 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU R 732 " 0.013 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 247 2.70 - 3.25: 8190 3.25 - 3.80: 12811 3.80 - 4.35: 15830 4.35 - 4.90: 27805 Nonbonded interactions: 64883 Sorted by model distance: nonbonded pdb=" O ARG R 573 " pdb=" NE2 GLN R 576 " model vdw 2.153 3.120 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.273 3.040 nonbonded pdb=" O GLY E 210 " pdb=" OG1 THR E 211 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASP R 687 " pdb=" N PHE R 688 " model vdw 2.286 3.120 nonbonded pdb=" O SER A 44 " pdb=" ND2 ASN A 144 " model vdw 2.329 3.120 ... (remaining 64878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.610 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 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 : 0.006 0.052 8945 Z= 0.372 Angle : 0.799 8.645 12111 Z= 0.485 Chirality : 0.052 0.344 1376 Planarity : 0.005 0.094 1530 Dihedral : 12.108 88.540 3205 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.73 % Allowed : 0.94 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1102 helix: 1.41 (0.29), residues: 345 sheet: 0.51 (0.31), residues: 272 loop : -1.35 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 63 HIS 0.010 0.002 HIS R 620 PHE 0.029 0.002 PHE B 234 TYR 0.035 0.003 TYR R 783 ARG 0.010 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 192 time to evaluate : 0.983 Fit side-chains REVERT: E 220 LEU cc_start: 0.8286 (mt) cc_final: 0.8057 (mt) REVERT: G 21 MET cc_start: 0.7486 (mtm) cc_final: 0.6849 (mtm) REVERT: R 551 THR cc_start: 0.7448 (m) cc_final: 0.7206 (m) REVERT: R 796 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6788 (mm-30) outliers start: 7 outliers final: 4 residues processed: 195 average time/residue: 0.2396 time to fit residues: 63.2462 Evaluate side-chains 179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 536 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 650 LEU Chi-restraints excluded: chain R residue 740 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.5980 chunk 82 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN R 539 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.153906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125944 restraints weight = 12939.647| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.76 r_work: 0.3505 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8945 Z= 0.212 Angle : 0.586 9.606 12111 Z= 0.316 Chirality : 0.043 0.154 1376 Planarity : 0.004 0.070 1530 Dihedral : 5.347 52.074 1217 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.01 % Rotamer: Outliers : 2.20 % Allowed : 6.07 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1102 helix: 2.15 (0.29), residues: 350 sheet: 0.65 (0.30), residues: 273 loop : -1.24 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 716 HIS 0.005 0.001 HIS R 786 PHE 0.016 0.002 PHE B 253 TYR 0.019 0.002 TYR R 783 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: B 63 TRP cc_start: 0.8184 (m100) cc_final: 0.7944 (m100) REVERT: B 75 GLN cc_start: 0.7028 (mt0) cc_final: 0.6476 (mt0) REVERT: B 293 ASN cc_start: 0.7742 (p0) cc_final: 0.7504 (p0) REVERT: E 83 MET cc_start: 0.6211 (ptp) cc_final: 0.5813 (ptp) REVERT: E 93 MET cc_start: 0.6536 (ttp) cc_final: 0.6332 (ttp) REVERT: E 98 ARG cc_start: 0.7885 (ttp-170) cc_final: 0.7607 (tmm160) REVERT: E 220 LEU cc_start: 0.8449 (mt) cc_final: 0.8176 (mt) REVERT: G 21 MET cc_start: 0.7834 (mtm) cc_final: 0.7142 (mtm) REVERT: R 650 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6490 (mp) REVERT: R 796 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6807 (mm-30) outliers start: 21 outliers final: 10 residues processed: 187 average time/residue: 0.2420 time to fit residues: 61.2526 Evaluate side-chains 182 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain R residue 644 VAL Chi-restraints excluded: chain R residue 650 LEU Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 183 HIS R 720 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124837 restraints weight = 13015.673| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.74 r_work: 0.3491 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8945 Z= 0.241 Angle : 0.581 9.034 12111 Z= 0.312 Chirality : 0.043 0.169 1376 Planarity : 0.004 0.060 1530 Dihedral : 4.950 54.860 1210 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 2.41 % Allowed : 8.47 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1102 helix: 2.31 (0.29), residues: 350 sheet: 0.68 (0.30), residues: 279 loop : -1.25 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.002 HIS R 786 PHE 0.019 0.002 PHE B 253 TYR 0.024 0.002 TYR R 783 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6753 (mmm) cc_final: 0.6201 (tmm) REVERT: B 46 ARG cc_start: 0.7962 (ttm110) cc_final: 0.7611 (ttp80) REVERT: E 83 MET cc_start: 0.6212 (ptp) cc_final: 0.5813 (ptp) REVERT: E 93 MET cc_start: 0.6883 (ttp) cc_final: 0.6675 (ttp) REVERT: E 98 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.7648 (tmm160) REVERT: E 220 LEU cc_start: 0.8411 (mt) cc_final: 0.8138 (mt) REVERT: G 21 MET cc_start: 0.7813 (mtm) cc_final: 0.7117 (mtm) REVERT: R 575 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7115 (pt) REVERT: R 796 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6786 (mm-30) outliers start: 23 outliers final: 13 residues processed: 184 average time/residue: 0.2338 time to fit residues: 57.4272 Evaluate side-chains 187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 644 VAL Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 720 GLN Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 95 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.0570 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 132 ASN R 539 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127326 restraints weight = 12883.067| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.73 r_work: 0.3526 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8945 Z= 0.158 Angle : 0.529 8.567 12111 Z= 0.284 Chirality : 0.042 0.155 1376 Planarity : 0.004 0.054 1530 Dihedral : 4.434 28.104 1208 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.63 % Favored : 97.28 % Rotamer: Outliers : 1.78 % Allowed : 10.15 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1102 helix: 2.50 (0.29), residues: 350 sheet: 0.74 (0.31), residues: 277 loop : -1.17 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS R 786 PHE 0.014 0.001 PHE A 74 TYR 0.028 0.001 TYR R 783 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6789 (mmm) cc_final: 0.6237 (tmm) REVERT: A 214 ASP cc_start: 0.7823 (m-30) cc_final: 0.7549 (m-30) REVERT: A 222 ASP cc_start: 0.7625 (t0) cc_final: 0.7322 (t0) REVERT: B 46 ARG cc_start: 0.7942 (ttm110) cc_final: 0.7603 (ttp80) REVERT: B 293 ASN cc_start: 0.7742 (p0) cc_final: 0.7505 (p0) REVERT: E 83 MET cc_start: 0.6145 (ptp) cc_final: 0.5787 (ptp) REVERT: E 220 LEU cc_start: 0.8416 (mt) cc_final: 0.8150 (mt) REVERT: G 21 MET cc_start: 0.7804 (mtm) cc_final: 0.7094 (mtm) REVERT: R 551 THR cc_start: 0.7438 (m) cc_final: 0.7099 (m) REVERT: R 596 ILE cc_start: 0.8135 (mt) cc_final: 0.7862 (tt) REVERT: R 796 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6763 (mm-30) outliers start: 17 outliers final: 12 residues processed: 179 average time/residue: 0.2412 time to fit residues: 58.5431 Evaluate side-chains 180 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 644 VAL Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 132 ASN R 539 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.152278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124340 restraints weight = 12964.452| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.70 r_work: 0.3481 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8945 Z= 0.258 Angle : 0.575 8.242 12111 Z= 0.311 Chirality : 0.043 0.177 1376 Planarity : 0.004 0.050 1530 Dihedral : 4.627 28.191 1208 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 2.62 % Allowed : 10.56 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1102 helix: 2.38 (0.29), residues: 350 sheet: 0.71 (0.31), residues: 277 loop : -1.24 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS R 786 PHE 0.020 0.002 PHE B 253 TYR 0.021 0.002 TYR R 783 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6787 (mmm) cc_final: 0.6216 (tmm) REVERT: B 46 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7605 (ttp80) REVERT: B 75 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6780 (mt0) REVERT: B 118 ASP cc_start: 0.6942 (p0) cc_final: 0.6728 (p0) REVERT: E 83 MET cc_start: 0.6206 (ptp) cc_final: 0.5852 (ptp) REVERT: E 93 MET cc_start: 0.6512 (ttp) cc_final: 0.6272 (ttp) REVERT: E 220 LEU cc_start: 0.8396 (mt) cc_final: 0.8115 (mt) REVERT: G 21 MET cc_start: 0.7844 (mtm) cc_final: 0.7136 (mtm) REVERT: R 551 THR cc_start: 0.7523 (m) cc_final: 0.7181 (m) REVERT: R 575 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7072 (pt) REVERT: R 796 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6747 (mm-30) outliers start: 25 outliers final: 17 residues processed: 190 average time/residue: 0.3337 time to fit residues: 86.1723 Evaluate side-chains 194 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 0.0770 chunk 79 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN R 539 HIS R 720 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.154429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.126401 restraints weight = 12861.629| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.73 r_work: 0.3517 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8945 Z= 0.179 Angle : 0.539 9.340 12111 Z= 0.289 Chirality : 0.042 0.153 1376 Planarity : 0.004 0.048 1530 Dihedral : 4.441 28.196 1208 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.01 % Rotamer: Outliers : 2.41 % Allowed : 10.77 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1102 helix: 2.58 (0.29), residues: 345 sheet: 0.76 (0.31), residues: 279 loop : -1.15 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS R 786 PHE 0.015 0.001 PHE A 74 TYR 0.019 0.001 TYR R 783 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6777 (mmm) cc_final: 0.6206 (tmm) REVERT: A 214 ASP cc_start: 0.7816 (m-30) cc_final: 0.7560 (m-30) REVERT: A 222 ASP cc_start: 0.7632 (t0) cc_final: 0.7311 (t0) REVERT: B 46 ARG cc_start: 0.7948 (ttm110) cc_final: 0.7602 (ttp80) REVERT: B 262 MET cc_start: 0.6228 (tpp) cc_final: 0.5955 (tpp) REVERT: B 293 ASN cc_start: 0.7744 (p0) cc_final: 0.7479 (p0) REVERT: E 83 MET cc_start: 0.6158 (ptp) cc_final: 0.5800 (ptp) REVERT: E 220 LEU cc_start: 0.8390 (mt) cc_final: 0.8123 (mt) REVERT: G 21 MET cc_start: 0.7819 (mtm) cc_final: 0.7141 (mtm) REVERT: R 551 THR cc_start: 0.7462 (m) cc_final: 0.7123 (m) REVERT: R 796 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6689 (mm-30) outliers start: 23 outliers final: 16 residues processed: 181 average time/residue: 0.2290 time to fit residues: 55.9501 Evaluate side-chains 180 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 639 PHE Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 89 optimal weight: 0.1980 chunk 108 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 75 GLN B 110 ASN B 132 ASN R 539 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.154129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126027 restraints weight = 12994.891| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.74 r_work: 0.3522 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8945 Z= 0.177 Angle : 0.535 7.907 12111 Z= 0.286 Chirality : 0.042 0.147 1376 Planarity : 0.004 0.047 1530 Dihedral : 4.381 28.465 1208 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 2.62 % Allowed : 11.09 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1102 helix: 2.62 (0.29), residues: 345 sheet: 0.80 (0.31), residues: 277 loop : -1.15 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS R 786 PHE 0.014 0.001 PHE A 74 TYR 0.020 0.001 TYR E 95 ARG 0.004 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6775 (mmm) cc_final: 0.6184 (tmm) REVERT: A 214 ASP cc_start: 0.7795 (m-30) cc_final: 0.7532 (m-30) REVERT: A 222 ASP cc_start: 0.7587 (t0) cc_final: 0.7282 (t0) REVERT: B 46 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7584 (ttp80) REVERT: B 293 ASN cc_start: 0.7721 (p0) cc_final: 0.7464 (p0) REVERT: E 83 MET cc_start: 0.6175 (ptp) cc_final: 0.5805 (ptp) REVERT: E 220 LEU cc_start: 0.8363 (mt) cc_final: 0.8093 (mt) REVERT: E 231 MET cc_start: 0.6989 (ttp) cc_final: 0.6253 (ttt) REVERT: G 21 MET cc_start: 0.7872 (mtm) cc_final: 0.7174 (mtm) REVERT: R 551 THR cc_start: 0.7466 (m) cc_final: 0.7134 (m) REVERT: R 596 ILE cc_start: 0.8154 (mt) cc_final: 0.7924 (tt) REVERT: R 796 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6788 (mm-30) outliers start: 25 outliers final: 20 residues processed: 182 average time/residue: 0.2235 time to fit residues: 54.7839 Evaluate side-chains 192 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 639 PHE Chi-restraints excluded: chain R residue 656 CYS Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 6 optimal weight: 0.0170 chunk 100 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 97 optimal weight: 0.0010 chunk 42 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 overall best weight: 0.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 539 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.155206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126989 restraints weight = 13138.278| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.81 r_work: 0.3535 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8945 Z= 0.150 Angle : 0.518 7.828 12111 Z= 0.277 Chirality : 0.041 0.143 1376 Planarity : 0.003 0.046 1530 Dihedral : 4.249 28.183 1208 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.72 % Favored : 97.19 % Rotamer: Outliers : 2.20 % Allowed : 11.72 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1102 helix: 2.68 (0.29), residues: 351 sheet: 0.83 (0.31), residues: 280 loop : -1.10 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 716 HIS 0.004 0.001 HIS R 786 PHE 0.013 0.001 PHE A 74 TYR 0.021 0.001 TYR E 95 ARG 0.004 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6763 (mmm) cc_final: 0.6188 (tmm) REVERT: A 222 ASP cc_start: 0.7578 (t0) cc_final: 0.7316 (t0) REVERT: B 46 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7585 (ttp80) REVERT: B 293 ASN cc_start: 0.7717 (p0) cc_final: 0.7460 (p0) REVERT: B 304 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7485 (tpp80) REVERT: E 18 ARG cc_start: 0.7822 (tpt-90) cc_final: 0.7535 (tpt-90) REVERT: E 83 MET cc_start: 0.6149 (ptp) cc_final: 0.5788 (ptp) REVERT: E 220 LEU cc_start: 0.8363 (mt) cc_final: 0.8096 (mt) REVERT: E 231 MET cc_start: 0.6898 (ttp) cc_final: 0.6168 (ttt) REVERT: G 21 MET cc_start: 0.7873 (mtm) cc_final: 0.7167 (mtm) REVERT: G 38 MET cc_start: 0.5614 (ptt) cc_final: 0.5212 (ptp) REVERT: R 551 THR cc_start: 0.7432 (m) cc_final: 0.7098 (m) REVERT: R 796 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6793 (mm-30) outliers start: 21 outliers final: 18 residues processed: 185 average time/residue: 0.2266 time to fit residues: 56.4674 Evaluate side-chains 187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 656 CYS Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 539 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.151909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123864 restraints weight = 13129.908| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.73 r_work: 0.3474 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8945 Z= 0.303 Angle : 0.617 8.746 12111 Z= 0.328 Chirality : 0.044 0.147 1376 Planarity : 0.004 0.046 1530 Dihedral : 4.609 28.475 1208 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.92 % Rotamer: Outliers : 2.20 % Allowed : 12.55 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1102 helix: 2.50 (0.29), residues: 351 sheet: 0.72 (0.31), residues: 263 loop : -1.15 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 716 HIS 0.006 0.002 HIS E 35 PHE 0.025 0.002 PHE B 253 TYR 0.041 0.002 TYR E 95 ARG 0.012 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6760 (mmm) cc_final: 0.6117 (tmm) REVERT: B 46 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7715 (ttp80) REVERT: B 293 ASN cc_start: 0.7735 (p0) cc_final: 0.7484 (p0) REVERT: E 83 MET cc_start: 0.6186 (ptp) cc_final: 0.5802 (ptp) REVERT: E 220 LEU cc_start: 0.8378 (mt) cc_final: 0.8121 (mt) REVERT: G 21 MET cc_start: 0.7890 (mtm) cc_final: 0.7225 (mtm) REVERT: R 551 THR cc_start: 0.7635 (m) cc_final: 0.7289 (m) REVERT: R 566 ILE cc_start: 0.7379 (mm) cc_final: 0.7159 (tp) REVERT: R 796 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6766 (mm-30) outliers start: 21 outliers final: 19 residues processed: 179 average time/residue: 0.2249 time to fit residues: 53.8749 Evaluate side-chains 187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 639 PHE Chi-restraints excluded: chain R residue 656 CYS Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 55 optimal weight: 0.4980 chunk 46 optimal weight: 0.0060 chunk 103 optimal weight: 0.0670 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.154559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126473 restraints weight = 13031.707| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.75 r_work: 0.3531 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8945 Z= 0.165 Angle : 0.570 12.057 12111 Z= 0.298 Chirality : 0.042 0.146 1376 Planarity : 0.004 0.046 1530 Dihedral : 4.354 28.091 1208 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.63 % Favored : 97.28 % Rotamer: Outliers : 1.88 % Allowed : 13.28 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1102 helix: 2.65 (0.29), residues: 351 sheet: 0.68 (0.31), residues: 282 loop : -1.11 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 716 HIS 0.005 0.001 HIS R 786 PHE 0.013 0.001 PHE A 74 TYR 0.030 0.001 TYR E 95 ARG 0.010 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6771 (mmm) cc_final: 0.6173 (tmm) REVERT: A 214 ASP cc_start: 0.7814 (m-30) cc_final: 0.7538 (m-30) REVERT: A 222 ASP cc_start: 0.7627 (t0) cc_final: 0.7346 (t0) REVERT: B 46 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7713 (ttp80) REVERT: B 137 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7349 (ttm170) REVERT: B 293 ASN cc_start: 0.7712 (p0) cc_final: 0.7436 (p0) REVERT: E 83 MET cc_start: 0.6137 (ptp) cc_final: 0.5764 (ptp) REVERT: E 220 LEU cc_start: 0.8353 (mt) cc_final: 0.8092 (mt) REVERT: G 21 MET cc_start: 0.7883 (mtm) cc_final: 0.7212 (mtm) REVERT: R 551 THR cc_start: 0.7474 (m) cc_final: 0.7140 (m) REVERT: R 566 ILE cc_start: 0.7178 (mm) cc_final: 0.6974 (tp) REVERT: R 796 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6775 (mm-30) outliers start: 18 outliers final: 18 residues processed: 176 average time/residue: 0.2267 time to fit residues: 54.1508 Evaluate side-chains 186 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 639 PHE Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 765 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124050 restraints weight = 13028.874| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.72 r_work: 0.3494 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8945 Z= 0.254 Angle : 0.607 12.966 12111 Z= 0.319 Chirality : 0.043 0.147 1376 Planarity : 0.004 0.045 1530 Dihedral : 4.513 28.269 1208 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 2.30 % Allowed : 12.87 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1102 helix: 2.55 (0.29), residues: 351 sheet: 0.69 (0.31), residues: 277 loop : -1.17 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS R 786 PHE 0.019 0.002 PHE B 253 TYR 0.021 0.002 TYR R 783 ARG 0.009 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4595.60 seconds wall clock time: 81 minutes 14.04 seconds (4874.04 seconds total)