Starting phenix.real_space_refine on Mon Mar 11 17:42:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydh_33747/03_2024/7ydh_33747_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydh_33747/03_2024/7ydh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydh_33747/03_2024/7ydh_33747.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydh_33747/03_2024/7ydh_33747.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydh_33747/03_2024/7ydh_33747_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydh_33747/03_2024/7ydh_33747_neut.pdb" } 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 Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 235": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.08, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.8 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: 0.98 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: 2.39 Time building geometry restraints manager: 3.50 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: 99.35 - 106.29: 168 106.29 - 113.23: 4824 113.23 - 120.17: 3319 120.17 - 127.10: 3703 127.10 - 134.04: 97 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 2.520 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.273 2.440 nonbonded pdb=" O GLY E 210 " pdb=" OG1 THR E 211 " model vdw 2.273 2.440 nonbonded pdb=" OD1 ASP R 687 " pdb=" N PHE R 688 " model vdw 2.286 2.520 nonbonded pdb=" O SER A 44 " pdb=" ND2 ASN A 144 " model vdw 2.329 2.520 ... (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 ========== 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: 0.900 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: 3.790 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.150 Find NCS groups from input model: 0.240 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.910 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 7 poor density : 192 time to evaluate : 1.160 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: 0.2251 time to fit residues: 58.6477 Evaluate side-chains 179 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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: 0.6980 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.0040 overall best weight: 0.2370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN R 778 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8945 Z= 0.142 Angle : 0.532 8.206 12111 Z= 0.284 Chirality : 0.042 0.152 1376 Planarity : 0.004 0.069 1530 Dihedral : 5.164 52.358 1217 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.54 % Favored : 97.37 % Rotamer: Outliers : 1.88 % Allowed : 6.17 % Favored : 91.95 % 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: 2.35 (0.29), residues: 346 sheet: 0.61 (0.30), residues: 282 loop : -1.12 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 716 HIS 0.004 0.001 HIS R 786 PHE 0.012 0.001 PHE R 533 TYR 0.020 0.001 TYR R 783 ARG 0.004 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 187 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 214 ASP cc_start: 0.7616 (m-30) cc_final: 0.7271 (m-30) REVERT: A 222 ASP cc_start: 0.7161 (t0) cc_final: 0.6843 (t0) REVERT: B 75 GLN cc_start: 0.6734 (mt0) cc_final: 0.6323 (mt0) REVERT: B 293 ASN cc_start: 0.7536 (p0) cc_final: 0.7203 (p0) REVERT: E 18 ARG cc_start: 0.7792 (tpt-90) cc_final: 0.7525 (tpt-90) REVERT: E 220 LEU cc_start: 0.8253 (mt) cc_final: 0.8052 (mt) REVERT: E 231 MET cc_start: 0.6857 (ttp) cc_final: 0.6331 (ttt) REVERT: G 21 MET cc_start: 0.7441 (mtm) cc_final: 0.6823 (mtm) REVERT: R 650 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6180 (mp) REVERT: R 796 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6708 (mm-30) outliers start: 18 outliers final: 10 residues processed: 179 average time/residue: 0.2260 time to fit residues: 54.5520 Evaluate side-chains 171 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 B residue 321 THR 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 762 ASP 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 55 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** R 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8945 Z= 0.268 Angle : 0.580 8.423 12111 Z= 0.313 Chirality : 0.043 0.163 1376 Planarity : 0.004 0.060 1530 Dihedral : 4.915 54.270 1210 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 2.72 % Allowed : 7.53 % Favored : 89.75 % 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: 0.65 (0.25), residues: 1102 helix: 2.30 (0.29), residues: 350 sheet: 0.72 (0.31), residues: 271 loop : -1.22 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.008 0.002 HIS R 620 PHE 0.021 0.002 PHE B 253 TYR 0.027 0.002 TYR R 783 ARG 0.003 0.000 ARG R 680 *********************** 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 208 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 182 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 214 ASP cc_start: 0.7639 (m-30) cc_final: 0.7348 (m-30) REVERT: B 63 TRP cc_start: 0.8020 (m100) cc_final: 0.7767 (m100) REVERT: B 293 ASN cc_start: 0.7643 (p0) cc_final: 0.7394 (p0) REVERT: G 21 MET cc_start: 0.7457 (mtm) cc_final: 0.6850 (mtm) REVERT: R 551 THR cc_start: 0.7500 (m) cc_final: 0.7215 (m) REVERT: R 575 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.6851 (pt) REVERT: R 796 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6736 (mm-30) outliers start: 26 outliers final: 14 residues processed: 191 average time/residue: 0.2304 time to fit residues: 59.2009 Evaluate side-chains 192 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 177 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 72 SER 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 173 THR Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 644 VAL Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 741 THR Chi-restraints excluded: chain R residue 762 ASP 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: 1.9990 chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN R 539 HIS ** R 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 778 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8945 Z= 0.248 Angle : 0.563 7.620 12111 Z= 0.302 Chirality : 0.043 0.151 1376 Planarity : 0.004 0.054 1530 Dihedral : 4.633 27.376 1208 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 2.93 % Allowed : 9.94 % Favored : 87.13 % 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: 0.68 (0.25), residues: 1102 helix: 2.34 (0.29), residues: 350 sheet: 0.70 (0.31), residues: 278 loop : -1.22 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS R 620 PHE 0.017 0.002 PHE B 253 TYR 0.022 0.002 TYR R 783 ARG 0.007 0.000 ARG B 96 *********************** 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 211 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6471 (mmm) cc_final: 0.5978 (tmm) REVERT: A 214 ASP cc_start: 0.7622 (m-30) cc_final: 0.7340 (m-30) REVERT: A 222 ASP cc_start: 0.7257 (t0) cc_final: 0.6921 (t0) REVERT: G 21 MET cc_start: 0.7449 (mtm) cc_final: 0.6845 (mtm) REVERT: R 551 THR cc_start: 0.7490 (m) cc_final: 0.7184 (m) REVERT: R 575 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.6945 (pt) REVERT: R 796 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6714 (mm-30) outliers start: 28 outliers final: 16 residues processed: 194 average time/residue: 0.2285 time to fit residues: 59.1551 Evaluate side-chains 192 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER 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 B residue 95 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 644 VAL Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 741 THR Chi-restraints excluded: chain R residue 762 ASP 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 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.0770 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 35 optimal weight: 0.0980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 293 ASN R 539 HIS R 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8945 Z= 0.150 Angle : 0.509 7.419 12111 Z= 0.271 Chirality : 0.041 0.166 1376 Planarity : 0.004 0.050 1530 Dihedral : 4.301 26.401 1208 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.01 % Rotamer: Outliers : 2.51 % Allowed : 10.67 % 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: 0.89 (0.26), residues: 1102 helix: 2.53 (0.29), residues: 350 sheet: 0.80 (0.31), residues: 277 loop : -1.08 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS R 620 PHE 0.016 0.001 PHE A 74 TYR 0.019 0.001 TYR E 95 ARG 0.004 0.000 ARG B 304 *********************** 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 205 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6524 (mmm) cc_final: 0.6020 (tmm) REVERT: A 214 ASP cc_start: 0.7577 (m-30) cc_final: 0.7234 (m-30) REVERT: A 222 ASP cc_start: 0.7184 (t0) cc_final: 0.6909 (t0) REVERT: B 63 TRP cc_start: 0.8114 (m100) cc_final: 0.7813 (m100) REVERT: E 18 ARG cc_start: 0.7787 (tpt-90) cc_final: 0.7527 (tpt-90) REVERT: G 21 MET cc_start: 0.7424 (mtm) cc_final: 0.6816 (mtm) REVERT: R 551 THR cc_start: 0.7350 (m) cc_final: 0.7068 (m) REVERT: R 575 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6769 (pt) REVERT: R 796 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6750 (mm-30) outliers start: 24 outliers final: 17 residues processed: 190 average time/residue: 0.2295 time to fit residues: 58.8314 Evaluate side-chains 194 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain R residue 537 MET Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 596 ILE Chi-restraints excluded: chain R residue 762 ASP 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 94 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.0030 chunk 26 optimal weight: 0.0980 chunk 105 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.0570 chunk 101 optimal weight: 4.9990 overall best weight: 0.1908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2134 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= 0.126 Angle : 0.487 6.599 12111 Z= 0.259 Chirality : 0.041 0.136 1376 Planarity : 0.003 0.047 1530 Dihedral : 4.076 26.231 1208 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.63 % Favored : 97.28 % Rotamer: Outliers : 2.51 % Allowed : 11.40 % 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: 0.96 (0.26), residues: 1102 helix: 2.46 (0.29), residues: 363 sheet: 0.93 (0.32), residues: 267 loop : -1.05 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 786 PHE 0.015 0.001 PHE A 74 TYR 0.016 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 196 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6534 (mmm) cc_final: 0.6071 (tmm) REVERT: A 214 ASP cc_start: 0.7453 (m-30) cc_final: 0.7086 (m-30) REVERT: B 63 TRP cc_start: 0.8046 (m100) cc_final: 0.7794 (m100) REVERT: B 304 ARG cc_start: 0.7403 (tpp80) cc_final: 0.7179 (tpp80) REVERT: E 231 MET cc_start: 0.6768 (ttp) cc_final: 0.6150 (ttt) REVERT: G 21 MET cc_start: 0.7431 (mtm) cc_final: 0.6809 (mtm) REVERT: R 575 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6358 (pt) REVERT: R 796 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6713 (mm-30) outliers start: 24 outliers final: 17 residues processed: 183 average time/residue: 0.2393 time to fit residues: 58.5555 Evaluate side-chains 188 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 234 LEU 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 762 ASP 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 11 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 0.0470 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 48 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8945 Z= 0.142 Angle : 0.505 10.346 12111 Z= 0.262 Chirality : 0.040 0.132 1376 Planarity : 0.003 0.047 1530 Dihedral : 4.038 26.261 1208 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 2.72 % Allowed : 12.24 % Favored : 85.04 % 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: 1.02 (0.26), residues: 1102 helix: 2.48 (0.29), residues: 363 sheet: 0.96 (0.31), residues: 280 loop : -1.05 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS R 786 PHE 0.014 0.001 PHE A 74 TYR 0.015 0.001 TYR R 783 ARG 0.008 0.000 ARG B 96 *********************** 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 195 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6541 (mmm) cc_final: 0.6070 (tmm) REVERT: A 214 ASP cc_start: 0.7450 (m-30) cc_final: 0.7079 (m-30) REVERT: A 222 ASP cc_start: 0.7130 (t0) cc_final: 0.6839 (t0) REVERT: B 63 TRP cc_start: 0.8056 (m100) cc_final: 0.7800 (m100) REVERT: B 304 ARG cc_start: 0.7422 (tpp80) cc_final: 0.7203 (tpp80) REVERT: E 231 MET cc_start: 0.6792 (ttp) cc_final: 0.6151 (ttt) REVERT: G 21 MET cc_start: 0.7416 (mtm) cc_final: 0.6802 (mtm) REVERT: R 551 THR cc_start: 0.7349 (m) cc_final: 0.7060 (m) REVERT: R 575 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6326 (pt) REVERT: R 796 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6898 (mm-30) outliers start: 26 outliers final: 21 residues processed: 181 average time/residue: 0.2335 time to fit residues: 57.0295 Evaluate side-chains 187 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 173 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 575 ILE Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 639 PHE Chi-restraints excluded: chain R residue 762 ASP 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 62 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8945 Z= 0.239 Angle : 0.551 7.534 12111 Z= 0.294 Chirality : 0.042 0.138 1376 Planarity : 0.004 0.045 1530 Dihedral : 4.325 26.715 1208 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.01 % Rotamer: Outliers : 2.93 % Allowed : 11.82 % 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: 0.91 (0.26), residues: 1102 helix: 2.47 (0.29), residues: 357 sheet: 0.78 (0.31), residues: 279 loop : -1.04 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS R 786 PHE 0.021 0.002 PHE B 253 TYR 0.017 0.002 TYR R 783 ARG 0.007 0.000 ARG B 96 *********************** 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 202 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6574 (mmm) cc_final: 0.6027 (tmm) REVERT: A 214 ASP cc_start: 0.7577 (m-30) cc_final: 0.7271 (m-30) REVERT: A 222 ASP cc_start: 0.7223 (t0) cc_final: 0.6960 (t0) REVERT: B 63 TRP cc_start: 0.8140 (m100) cc_final: 0.7809 (m100) REVERT: G 21 MET cc_start: 0.7499 (mtm) cc_final: 0.6920 (mtm) REVERT: R 551 THR cc_start: 0.7530 (m) cc_final: 0.7229 (m) REVERT: R 566 ILE cc_start: 0.7565 (mm) cc_final: 0.7326 (tp) REVERT: R 575 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6678 (pt) REVERT: R 796 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6880 (mm-30) outliers start: 28 outliers final: 24 residues processed: 186 average time/residue: 0.2310 time to fit residues: 57.4736 Evaluate side-chains 196 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 171 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER 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 A residue 201 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 173 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 575 ILE Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 596 ILE Chi-restraints excluded: chain R residue 639 PHE Chi-restraints excluded: chain R residue 644 VAL Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 762 ASP 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 97 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 chunk 58 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 88 optimal weight: 0.3980 chunk 92 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8945 Z= 0.138 Angle : 0.504 8.031 12111 Z= 0.264 Chirality : 0.041 0.132 1376 Planarity : 0.003 0.046 1530 Dihedral : 4.097 26.650 1208 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 2.41 % Allowed : 12.34 % 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: 1.04 (0.26), residues: 1102 helix: 2.58 (0.29), residues: 357 sheet: 0.86 (0.31), residues: 278 loop : -0.97 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 177 HIS 0.005 0.001 HIS R 786 PHE 0.013 0.001 PHE A 74 TYR 0.016 0.001 TYR R 783 ARG 0.007 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 fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6551 (mmm) cc_final: 0.6032 (tmm) REVERT: A 214 ASP cc_start: 0.7484 (m-30) cc_final: 0.7111 (m-30) REVERT: A 222 ASP cc_start: 0.7167 (t0) cc_final: 0.6934 (t0) REVERT: B 63 TRP cc_start: 0.8082 (m100) cc_final: 0.7784 (m100) REVERT: G 21 MET cc_start: 0.7480 (mtm) cc_final: 0.6913 (mtm) REVERT: R 551 THR cc_start: 0.7396 (m) cc_final: 0.7105 (m) REVERT: R 566 ILE cc_start: 0.7378 (mm) cc_final: 0.7149 (tp) REVERT: R 575 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6406 (pt) REVERT: R 796 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6861 (mm-30) outliers start: 23 outliers final: 20 residues processed: 177 average time/residue: 0.2367 time to fit residues: 55.7268 Evaluate side-chains 190 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 173 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 575 ILE Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 639 PHE Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 762 ASP 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 49 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2171 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= 0.224 Angle : 0.567 11.158 12111 Z= 0.298 Chirality : 0.042 0.135 1376 Planarity : 0.004 0.045 1530 Dihedral : 4.331 27.010 1208 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 2.62 % Allowed : 12.66 % Favored : 84.73 % 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: 2.50 (0.29), residues: 357 sheet: 0.72 (0.31), residues: 278 loop : -1.04 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS R 786 PHE 0.017 0.002 PHE B 253 TYR 0.017 0.002 TYR E 95 ARG 0.006 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 193 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.6577 (mmm) cc_final: 0.6002 (tmm) REVERT: A 214 ASP cc_start: 0.7569 (m-30) cc_final: 0.7257 (m-30) REVERT: A 222 ASP cc_start: 0.7222 (t0) cc_final: 0.6968 (t0) REVERT: B 63 TRP cc_start: 0.8126 (m100) cc_final: 0.7802 (m100) REVERT: B 262 MET cc_start: 0.5731 (tpp) cc_final: 0.5364 (tpp) REVERT: E 93 MET cc_start: 0.5288 (ttp) cc_final: 0.5082 (ttp) REVERT: G 21 MET cc_start: 0.7517 (mtm) cc_final: 0.6916 (mtm) REVERT: R 551 THR cc_start: 0.7524 (m) cc_final: 0.7226 (m) REVERT: R 566 ILE cc_start: 0.7567 (mm) cc_final: 0.7331 (tp) REVERT: R 575 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6651 (pt) REVERT: R 796 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6886 (mm-30) outliers start: 25 outliers final: 22 residues processed: 179 average time/residue: 0.2289 time to fit residues: 54.8009 Evaluate side-chains 191 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER 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 201 THR 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 164 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 576 GLN Chi-restraints excluded: chain R residue 639 PHE Chi-restraints excluded: chain R residue 705 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 762 ASP 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 79 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 0.0070 chunk 36 optimal weight: 0.1980 chunk 88 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.155509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127788 restraints weight = 12870.005| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.73 r_work: 0.3543 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8945 Z= 0.142 Angle : 0.531 11.027 12111 Z= 0.274 Chirality : 0.041 0.132 1376 Planarity : 0.003 0.045 1530 Dihedral : 4.128 26.795 1208 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 2.82 % Allowed : 12.55 % Favored : 84.62 % 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: 1.03 (0.26), residues: 1102 helix: 2.62 (0.29), residues: 357 sheet: 0.78 (0.31), residues: 278 loop : -0.96 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS R 786 PHE 0.013 0.001 PHE A 74 TYR 0.016 0.001 TYR R 783 ARG 0.006 0.000 ARG A 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2286.01 seconds wall clock time: 41 minutes 57.22 seconds (2517.22 seconds total)