Starting phenix.real_space_refine on Thu Feb 15 12:11:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kl9_0704/02_2024/6kl9_0704_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kl9_0704/02_2024/6kl9_0704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kl9_0704/02_2024/6kl9_0704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kl9_0704/02_2024/6kl9_0704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kl9_0704/02_2024/6kl9_0704_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kl9_0704/02_2024/6kl9_0704_neut.pdb" } resolution = 3.25 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 2 5.21 5 S 39 5.16 5 C 7722 2.51 5 N 2005 2.21 5 O 2398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 133": "OD1" <-> "OD2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 737": "NH1" <-> "NH2" Residue "A TYR 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A GLU 925": "OE1" <-> "OE2" Residue "A PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1112": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12191 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1180, 9711 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 1155} Chain breaks: 6 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 1180, 9711 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 1155} Chain breaks: 6 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 9895 Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "G" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 529 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 9, 'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 6} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS A 775 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 775 " occ=0.50 Time building chain proxies: 10.85, per 1000 atoms: 0.89 Number of scatterers: 12191 At special positions: 0 Unit cell: (124.2, 125.28, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 25 15.00 Mg 2 11.99 O 2398 8.00 N 2005 7.00 C 7722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS C 131 " 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: 4.86 Conformation dependent library (CDL) restraints added in 3.8 seconds 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 15 sheets defined 46.3% alpha, 10.5% beta 4 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.700A pdb=" N LYS A 6 " --> pdb=" O LYS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 46 through 66 removed outlier: 3.762A pdb=" N VAL A 50 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.539A pdb=" N TYR A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 112 removed outlier: 4.446A pdb=" N ASN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.680A pdb=" N ILE A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 178 through 194 removed outlier: 4.108A pdb=" N ARG A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 removed outlier: 3.508A pdb=" N LYS A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.679A pdb=" N GLU A 221 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.895A pdb=" N ILE A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 removed outlier: 4.422A pdb=" N ASN A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.641A pdb=" N LEU A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 325 Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.890A pdb=" N THR A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.921A pdb=" N ILE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 removed outlier: 3.643A pdb=" N GLU A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 409 through 432 Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.615A pdb=" N VAL A 453 " --> pdb=" O ASN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 493 through 512 removed outlier: 4.109A pdb=" N LEU A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.831A pdb=" N GLN A 567 " --> pdb=" O LYS A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 591 removed outlier: 4.342A pdb=" N LYS A 591 " --> pdb=" O GLY A 588 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 588 through 591' Processing helix chain 'A' and resid 592 through 598 removed outlier: 4.034A pdb=" N VAL A 596 " --> pdb=" O MET A 592 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 619 Processing helix chain 'A' and resid 629 through 642 Processing helix chain 'A' and resid 666 through 676 Processing helix chain 'A' and resid 686 through 697 removed outlier: 4.052A pdb=" N VAL A 690 " --> pdb=" O SER A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 710 Processing helix chain 'A' and resid 718 through 726 removed outlier: 3.699A pdb=" N MET A 722 " --> pdb=" O ASN A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 756 removed outlier: 3.874A pdb=" N LEU A 756 " --> pdb=" O LYS A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 790 removed outlier: 3.648A pdb=" N PHE A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 790 " --> pdb=" O LYS A 787 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 786 through 790' Processing helix chain 'A' and resid 811 through 822 removed outlier: 3.573A pdb=" N GLU A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.795A pdb=" N GLU A 885 " --> pdb=" O LYS A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 919 removed outlier: 3.852A pdb=" N GLU A 894 " --> pdb=" O TRP A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 954 Processing helix chain 'A' and resid 1021 through 1031 Processing helix chain 'A' and resid 1091 through 1100 Processing helix chain 'A' and resid 1101 through 1104 removed outlier: 4.180A pdb=" N ILE A1104 " --> pdb=" O LYS A1101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1101 through 1104' Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1120 through 1135 removed outlier: 4.478A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1167 Processing helix chain 'A' and resid 1178 through 1199 removed outlier: 3.612A pdb=" N ASN A1182 " --> pdb=" O ASN A1178 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A1199 " --> pdb=" O ILE A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1209 removed outlier: 3.646A pdb=" N VAL A1209 " --> pdb=" O LEU A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1225 Processing helix chain 'B' and resid 118 through 149 removed outlier: 3.869A pdb=" N LEU B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 3.506A pdb=" N LEU B 232 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 150 removed outlier: 4.026A pdb=" N LEU C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.754A pdb=" N LEU C 170 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.827A pdb=" N ARG C 203 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU C 204 " --> pdb=" O THR C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 200 through 204' Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.586A pdb=" N LEU C 232 " --> pdb=" O VAL C 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.688A pdb=" N PHE A 521 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 20 " --> pdb=" O TYR A 705 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE A 546 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.688A pdb=" N PHE A 521 " --> pdb=" O MET A 746 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 removed outlier: 3.814A pdb=" N PHE A 244 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 252 " --> pdb=" O PHE A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AA5, first strand: chain 'A' and resid 758 through 759 Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AA7, first strand: chain 'A' and resid 850 through 855 Processing sheet with id=AA8, first strand: chain 'A' and resid 858 through 863 Processing sheet with id=AA9, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 3.627A pdb=" N ALA A1046 " --> pdb=" O ARG A1033 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1070 through 1073 Processing sheet with id=AB2, first strand: chain 'A' and resid 1138 through 1140 Processing sheet with id=AB3, first strand: chain 'B' and resid 180 through 181 removed outlier: 3.788A pdb=" N GLU B 180 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 183 through 187 removed outlier: 4.917A pdb=" N CYS B 185 " --> pdb=" O CYS B 195 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N CYS B 195 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 158 through 161 Processing sheet with id=AB6, first strand: chain 'C' and resid 183 through 187 removed outlier: 3.502A pdb=" N TYR C 197 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS C 185 " --> pdb=" O CYS C 195 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N CYS C 195 " --> pdb=" O CYS C 185 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 14 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3559 1.34 - 1.46: 3047 1.46 - 1.58: 5760 1.58 - 1.71: 48 1.71 - 1.83: 63 Bond restraints: 12477 Sorted by residual: bond pdb=" C LEU A 128 " pdb=" N PRO A 129 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.20e-02 6.94e+03 5.14e+00 bond pdb=" CA VAL B 216 " pdb=" C VAL B 216 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.27e-02 6.20e+03 3.71e+00 bond pdb=" N ARG B 187 " pdb=" CA ARG B 187 " ideal model delta sigma weight residual 1.454 1.476 -0.021 1.15e-02 7.56e+03 3.48e+00 bond pdb=" C GLY A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.331 1.346 -0.015 7.90e-03 1.60e+04 3.40e+00 bond pdb=" C TYR B 144 " pdb=" O TYR B 144 " ideal model delta sigma weight residual 1.237 1.217 0.020 1.19e-02 7.06e+03 2.74e+00 ... (remaining 12472 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.64: 381 106.64 - 113.51: 6540 113.51 - 120.37: 5205 120.37 - 127.24: 4655 127.24 - 134.10: 132 Bond angle restraints: 16913 Sorted by residual: angle pdb=" N PHE A 131 " pdb=" CA PHE A 131 " pdb=" C PHE A 131 " ideal model delta sigma weight residual 111.03 121.19 -10.16 1.11e+00 8.12e-01 8.38e+01 angle pdb=" N ASP A 450 " pdb=" CA ASP A 450 " pdb=" C ASP A 450 " ideal model delta sigma weight residual 111.28 120.45 -9.17 1.09e+00 8.42e-01 7.07e+01 angle pdb=" N LEU A1047 " pdb=" CA LEU A1047 " pdb=" C LEU A1047 " ideal model delta sigma weight residual 108.48 122.70 -14.22 1.80e+00 3.09e-01 6.24e+01 angle pdb=" N VAL A 758 " pdb=" CA VAL A 758 " pdb=" C VAL A 758 " ideal model delta sigma weight residual 108.27 118.12 -9.85 1.37e+00 5.33e-01 5.17e+01 angle pdb=" N HIS C 190 " pdb=" CA HIS C 190 " pdb=" C HIS C 190 " ideal model delta sigma weight residual 114.75 106.59 8.16 1.26e+00 6.30e-01 4.20e+01 ... (remaining 16908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 7475 35.95 - 71.90: 125 71.90 - 107.86: 9 107.86 - 143.81: 2 143.81 - 179.76: 3 Dihedral angle restraints: 7614 sinusoidal: 3412 harmonic: 4202 Sorted by residual: dihedral pdb=" O4' C G 21 " pdb=" C1' C G 21 " pdb=" N1 C G 21 " pdb=" C2 C G 21 " ideal model delta sinusoidal sigma weight residual -128.00 51.76 -179.76 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U G 14 " pdb=" C1' U G 14 " pdb=" N1 U G 14 " pdb=" C2 U G 14 " ideal model delta sinusoidal sigma weight residual -128.00 50.39 -178.39 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS C 131 " pdb=" CB CYS C 131 " ideal model delta sinusoidal sigma weight residual -86.00 -141.09 55.09 1 1.00e+01 1.00e-02 4.11e+01 ... (remaining 7611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1685 0.099 - 0.198: 134 0.198 - 0.298: 20 0.298 - 0.397: 4 0.397 - 0.496: 2 Chirality restraints: 1845 Sorted by residual: chirality pdb=" CA ASN A 928 " pdb=" N ASN A 928 " pdb=" C ASN A 928 " pdb=" CB ASN A 928 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" CA LEU A1047 " pdb=" N LEU A1047 " pdb=" C LEU A1047 " pdb=" CB LEU A1047 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CB VAL A 228 " pdb=" CA VAL A 228 " pdb=" CG1 VAL A 228 " pdb=" CG2 VAL A 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 1842 not shown) Planarity restraints: 2077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 991 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLY A 991 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY A 991 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 992 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 720 " 0.021 2.00e-02 2.50e+03 2.58e-02 9.98e+00 pdb=" CG HIS A 720 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS A 720 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS A 720 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS A 720 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS A 720 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 527 " -0.050 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO A 528 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 528 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 528 " -0.042 5.00e-02 4.00e+02 ... (remaining 2074 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 96 2.60 - 3.18: 9696 3.18 - 3.75: 17176 3.75 - 4.33: 24374 4.33 - 4.90: 39653 Nonbonded interactions: 90995 Sorted by model distance: nonbonded pdb="MG MG G 101 " pdb=" O HOH G 202 " model vdw 2.031 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 205 " model vdw 2.035 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 204 " model vdw 2.036 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 206 " model vdw 2.045 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 201 " model vdw 2.046 2.170 ... (remaining 90990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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=0.50 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: 0.990 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: 4.180 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 44.530 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.080 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 : 0.005 0.051 12477 Z= 0.288 Angle : 1.009 14.216 16913 Z= 0.606 Chirality : 0.063 0.496 1845 Planarity : 0.007 0.077 2077 Dihedral : 13.562 179.759 4899 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.74 % Favored : 90.04 % Rotamer: Outliers : 2.72 % Allowed : 2.95 % Favored : 94.33 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % 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: -4.82 (0.16), residues: 1399 helix: -3.28 (0.13), residues: 585 sheet: -0.77 (0.57), residues: 87 loop : -3.52 (0.18), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A1218 HIS 0.031 0.002 HIS A 720 PHE 0.027 0.002 PHE A 474 TYR 0.027 0.002 TYR A1049 ARG 0.009 0.001 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 342 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.7748 (t70) cc_final: 0.7458 (t-90) REVERT: A 107 LYS cc_start: 0.8050 (tptm) cc_final: 0.7436 (tttm) REVERT: A 135 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7582 (mmtt) REVERT: A 179 ASN cc_start: 0.7659 (m-40) cc_final: 0.7434 (m-40) REVERT: A 278 LYS cc_start: 0.7699 (mppt) cc_final: 0.7007 (pttp) REVERT: A 875 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8131 (tp) REVERT: A 878 LYS cc_start: 0.7812 (mtmt) cc_final: 0.7477 (tttt) REVERT: A 925 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8091 (pp20) REVERT: A 1003 LYS cc_start: 0.8200 (mtmp) cc_final: 0.7870 (mtpt) REVERT: A 1112 ARG cc_start: 0.5316 (OUTLIER) cc_final: 0.4992 (ttp-170) REVERT: A 1131 MET cc_start: 0.7577 (mmm) cc_final: 0.7312 (mmt) REVERT: A 1133 LEU cc_start: 0.8255 (mp) cc_final: 0.7973 (tp) REVERT: A 1134 MET cc_start: 0.7236 (ttp) cc_final: 0.6944 (ttp) REVERT: A 1137 MET cc_start: 0.7040 (ttm) cc_final: 0.6830 (mtp) REVERT: A 1204 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 132 ILE cc_start: 0.8202 (mt) cc_final: 0.7995 (mt) REVERT: B 134 LYS cc_start: 0.7596 (mttm) cc_final: 0.6961 (mttt) REVERT: B 158 VAL cc_start: 0.8604 (t) cc_final: 0.8127 (m) REVERT: B 166 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6827 (p0) REVERT: B 169 ASN cc_start: 0.7894 (t0) cc_final: 0.7569 (t0) REVERT: B 188 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7926 (t80) REVERT: B 209 TYR cc_start: 0.8462 (m-80) cc_final: 0.8129 (m-10) REVERT: B 217 ARG cc_start: 0.7799 (ptt-90) cc_final: 0.7515 (ptt-90) REVERT: B 222 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7149 (mtm-85) outliers start: 34 outliers final: 22 residues processed: 371 average time/residue: 0.2718 time to fit residues: 138.5573 Evaluate side-chains 226 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1033 ARG Chi-restraints excluded: chain A residue 1035 MET Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1112 ARG Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 222 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.0370 chunk 107 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 268 GLN A 582 ASN A 803 ASN A 813 ASN A 955 ASN A 963 ASN A 989 GLN A1012 ASN C 145 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12477 Z= 0.208 Angle : 0.640 8.823 16913 Z= 0.348 Chirality : 0.044 0.268 1845 Planarity : 0.005 0.061 2077 Dihedral : 15.034 177.001 1991 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.52 % Favored : 91.33 % Rotamer: Outliers : 2.80 % Allowed : 10.57 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.87 (0.20), residues: 1399 helix: -0.84 (0.19), residues: 583 sheet: -1.24 (0.52), residues: 102 loop : -3.04 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1218 HIS 0.018 0.002 HIS A 720 PHE 0.032 0.002 PHE A 173 TYR 0.020 0.002 TYR A1036 ARG 0.005 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 215 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.7777 (t70) cc_final: 0.7445 (t70) REVERT: A 107 LYS cc_start: 0.7783 (tptm) cc_final: 0.7329 (tttt) REVERT: A 268 GLN cc_start: 0.6783 (mm-40) cc_final: 0.5600 (mm-40) REVERT: A 278 LYS cc_start: 0.7570 (mppt) cc_final: 0.7240 (pttp) REVERT: A 386 ARG cc_start: 0.6649 (ttm110) cc_final: 0.6410 (mtm180) REVERT: A 481 ASN cc_start: 0.7557 (p0) cc_final: 0.7328 (p0) REVERT: A 558 MET cc_start: 0.6590 (mpt) cc_final: 0.6358 (mpt) REVERT: A 592 MET cc_start: 0.5562 (mmt) cc_final: 0.5271 (mmt) REVERT: A 765 ILE cc_start: 0.6859 (pt) cc_final: 0.6436 (tp) REVERT: A 875 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8073 (tp) REVERT: A 1031 PHE cc_start: 0.7123 (m-80) cc_final: 0.6834 (m-80) REVERT: A 1133 LEU cc_start: 0.8348 (mp) cc_final: 0.7975 (tt) REVERT: B 125 GLN cc_start: 0.7662 (mt0) cc_final: 0.6965 (pt0) REVERT: B 166 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6667 (p0) REVERT: B 169 ASN cc_start: 0.7895 (t0) cc_final: 0.7461 (t0) REVERT: B 188 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8238 (t80) outliers start: 35 outliers final: 19 residues processed: 242 average time/residue: 0.2339 time to fit residues: 83.0558 Evaluate side-chains 190 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 129 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 128 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 142 ASN A 797 HIS A 803 ASN A 975 GLN B 145 ASN C 145 ASN C 193 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12477 Z= 0.232 Angle : 0.616 8.513 16913 Z= 0.334 Chirality : 0.044 0.210 1845 Planarity : 0.004 0.052 2077 Dihedral : 14.156 177.454 1940 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.10 % Favored : 90.76 % Rotamer: Outliers : 3.57 % Allowed : 11.34 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.12 (0.21), residues: 1399 helix: 0.11 (0.21), residues: 585 sheet: -1.53 (0.45), residues: 127 loop : -2.85 (0.20), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1218 HIS 0.017 0.002 HIS A 720 PHE 0.051 0.002 PHE A1027 TYR 0.019 0.002 TYR A1185 ARG 0.004 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 190 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.7527 (t70) cc_final: 0.7325 (t-90) REVERT: A 99 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7275 (mt) REVERT: A 107 LYS cc_start: 0.7974 (tptm) cc_final: 0.7554 (ttpt) REVERT: A 278 LYS cc_start: 0.7724 (mppt) cc_final: 0.7284 (pttp) REVERT: A 399 GLN cc_start: 0.5619 (tt0) cc_final: 0.5403 (tt0) REVERT: A 471 LYS cc_start: 0.7893 (tmmt) cc_final: 0.7536 (tttp) REVERT: A 481 ASN cc_start: 0.7602 (p0) cc_final: 0.7306 (p0) REVERT: A 558 MET cc_start: 0.6718 (mpt) cc_final: 0.6503 (mpt) REVERT: A 592 MET cc_start: 0.5609 (OUTLIER) cc_final: 0.5376 (mmt) REVERT: A 875 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8095 (tp) REVERT: A 882 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7770 (tt0) REVERT: A 1035 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5694 (ttp) REVERT: A 1133 LEU cc_start: 0.8369 (mp) cc_final: 0.7946 (tt) REVERT: B 125 GLN cc_start: 0.7642 (mt0) cc_final: 0.6951 (pt0) REVERT: B 129 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7822 (mmt90) REVERT: B 166 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6596 (p0) REVERT: B 169 ASN cc_start: 0.7956 (t0) cc_final: 0.7680 (t0) REVERT: B 188 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8281 (t80) REVERT: C 196 PHE cc_start: 0.6171 (m-10) cc_final: 0.5795 (m-10) REVERT: C 231 ASN cc_start: 0.5702 (m-40) cc_final: 0.5355 (m110) outliers start: 45 outliers final: 30 residues processed: 222 average time/residue: 0.2301 time to fit residues: 75.9021 Evaluate side-chains 210 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 975 GLN Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1035 MET Chi-restraints excluded: chain A residue 1055 THR Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 0.0170 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12477 Z= 0.245 Angle : 0.617 8.597 16913 Z= 0.334 Chirality : 0.044 0.217 1845 Planarity : 0.004 0.048 2077 Dihedral : 14.095 177.028 1937 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.52 % Favored : 91.33 % Rotamer: Outliers : 3.50 % Allowed : 12.67 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.80 (0.22), residues: 1399 helix: 0.53 (0.21), residues: 586 sheet: -1.65 (0.43), residues: 133 loop : -2.78 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1086 HIS 0.018 0.002 HIS A 720 PHE 0.060 0.002 PHE A1027 TYR 0.030 0.002 TYR A 974 ARG 0.003 0.001 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 197 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.7525 (t70) cc_final: 0.7280 (t-90) REVERT: A 107 LYS cc_start: 0.7959 (tptm) cc_final: 0.7559 (tttt) REVERT: A 268 GLN cc_start: 0.6527 (mm-40) cc_final: 0.5512 (mt0) REVERT: A 368 ASP cc_start: 0.6061 (OUTLIER) cc_final: 0.5509 (m-30) REVERT: A 471 LYS cc_start: 0.7910 (tmmt) cc_final: 0.7576 (tttp) REVERT: A 558 MET cc_start: 0.6763 (mpt) cc_final: 0.6552 (mpt) REVERT: A 592 MET cc_start: 0.5590 (OUTLIER) cc_final: 0.5339 (mmt) REVERT: A 875 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8096 (tp) REVERT: A 1133 LEU cc_start: 0.8355 (mp) cc_final: 0.7851 (tt) REVERT: B 125 GLN cc_start: 0.7755 (mt0) cc_final: 0.6872 (pt0) REVERT: B 166 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6667 (p0) REVERT: B 169 ASN cc_start: 0.7981 (t0) cc_final: 0.7653 (t0) outliers start: 44 outliers final: 35 residues processed: 228 average time/residue: 0.2339 time to fit residues: 78.0064 Evaluate side-chains 217 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 178 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 0.1980 chunk 117 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 0 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN C 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12477 Z= 0.196 Angle : 0.585 8.910 16913 Z= 0.317 Chirality : 0.043 0.215 1845 Planarity : 0.004 0.046 2077 Dihedral : 14.003 177.858 1937 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.81 % Favored : 91.05 % Rotamer: Outliers : 3.81 % Allowed : 13.44 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.47 (0.22), residues: 1399 helix: 0.83 (0.22), residues: 586 sheet: -1.31 (0.46), residues: 119 loop : -2.65 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1193 HIS 0.013 0.001 HIS A 720 PHE 0.049 0.002 PHE A1027 TYR 0.017 0.001 TYR C 121 ARG 0.003 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 194 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.7559 (t70) cc_final: 0.7286 (t-90) REVERT: A 107 LYS cc_start: 0.7857 (tptm) cc_final: 0.7472 (ttpt) REVERT: A 268 GLN cc_start: 0.6731 (mm-40) cc_final: 0.5618 (mt0) REVERT: A 320 LYS cc_start: 0.6775 (mttp) cc_final: 0.6505 (mtpt) REVERT: A 368 ASP cc_start: 0.5917 (OUTLIER) cc_final: 0.5382 (m-30) REVERT: A 386 ARG cc_start: 0.6209 (ttp-110) cc_final: 0.5893 (mtm-85) REVERT: A 401 GLN cc_start: 0.7420 (tm-30) cc_final: 0.7108 (tt0) REVERT: A 471 LYS cc_start: 0.7858 (tmmt) cc_final: 0.7514 (tttp) REVERT: A 558 MET cc_start: 0.6728 (mpt) cc_final: 0.6510 (mpt) REVERT: A 592 MET cc_start: 0.5533 (OUTLIER) cc_final: 0.5284 (mmt) REVERT: A 875 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8070 (tp) REVERT: A 1133 LEU cc_start: 0.8364 (mp) cc_final: 0.8111 (tp) REVERT: B 125 GLN cc_start: 0.7738 (mt0) cc_final: 0.6912 (pt0) REVERT: B 166 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6582 (p0) REVERT: B 169 ASN cc_start: 0.8031 (t0) cc_final: 0.7686 (t0) REVERT: B 211 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7283 (t) outliers start: 48 outliers final: 39 residues processed: 229 average time/residue: 0.2329 time to fit residues: 78.2648 Evaluate side-chains 223 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 179 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 0.0670 chunk 132 optimal weight: 0.8980 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12477 Z= 0.219 Angle : 0.605 11.079 16913 Z= 0.327 Chirality : 0.043 0.227 1845 Planarity : 0.004 0.063 2077 Dihedral : 13.992 176.969 1937 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.03 % Favored : 90.83 % Rotamer: Outliers : 3.96 % Allowed : 14.53 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.22), residues: 1399 helix: 1.02 (0.22), residues: 581 sheet: -1.39 (0.44), residues: 125 loop : -2.55 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 534 HIS 0.016 0.002 HIS A 720 PHE 0.038 0.002 PHE A1027 TYR 0.017 0.001 TYR A1185 ARG 0.007 0.001 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 188 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.7485 (t70) cc_final: 0.7246 (t-90) REVERT: A 107 LYS cc_start: 0.7829 (tptm) cc_final: 0.7494 (ttpt) REVERT: A 268 GLN cc_start: 0.6615 (mm-40) cc_final: 0.5670 (mt0) REVERT: A 320 LYS cc_start: 0.6813 (mttp) cc_final: 0.6550 (mtpt) REVERT: A 333 SER cc_start: 0.8627 (p) cc_final: 0.8312 (t) REVERT: A 368 ASP cc_start: 0.6013 (OUTLIER) cc_final: 0.5478 (m-30) REVERT: A 386 ARG cc_start: 0.6242 (ttp-110) cc_final: 0.5891 (mtm-85) REVERT: A 401 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7240 (tt0) REVERT: A 471 LYS cc_start: 0.7875 (tmmt) cc_final: 0.7551 (tttp) REVERT: A 552 LYS cc_start: 0.5569 (OUTLIER) cc_final: 0.5257 (mtmm) REVERT: A 558 MET cc_start: 0.6779 (mpt) cc_final: 0.6558 (mpt) REVERT: A 592 MET cc_start: 0.5377 (mmt) cc_final: 0.5153 (mmt) REVERT: A 875 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8081 (tp) REVERT: A 1133 LEU cc_start: 0.8349 (mp) cc_final: 0.8027 (tp) REVERT: B 125 GLN cc_start: 0.7749 (mt0) cc_final: 0.6810 (pt0) REVERT: B 166 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6420 (p0) REVERT: B 169 ASN cc_start: 0.8014 (t0) cc_final: 0.7424 (t0) outliers start: 50 outliers final: 38 residues processed: 225 average time/residue: 0.2217 time to fit residues: 74.3415 Evaluate side-chains 219 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 177 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 0.0670 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12477 Z= 0.176 Angle : 0.580 10.201 16913 Z= 0.313 Chirality : 0.043 0.208 1845 Planarity : 0.004 0.046 2077 Dihedral : 13.913 178.248 1935 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.24 % Favored : 91.62 % Rotamer: Outliers : 3.19 % Allowed : 15.62 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.23), residues: 1399 helix: 1.27 (0.22), residues: 573 sheet: -1.29 (0.41), residues: 145 loop : -2.43 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 362 HIS 0.010 0.001 HIS A 720 PHE 0.045 0.001 PHE A1027 TYR 0.019 0.001 TYR A1036 ARG 0.003 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 185 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7047 (mmt180) cc_final: 0.6740 (mmt180) REVERT: A 67 HIS cc_start: 0.7497 (t70) cc_final: 0.7175 (t-90) REVERT: A 107 LYS cc_start: 0.7844 (tptm) cc_final: 0.7564 (ttpt) REVERT: A 268 GLN cc_start: 0.6574 (mm-40) cc_final: 0.5171 (mm-40) REVERT: A 333 SER cc_start: 0.8579 (p) cc_final: 0.8306 (t) REVERT: A 368 ASP cc_start: 0.6016 (OUTLIER) cc_final: 0.5518 (m-30) REVERT: A 386 ARG cc_start: 0.6195 (ttp-110) cc_final: 0.5797 (mtm-85) REVERT: A 401 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7205 (tt0) REVERT: A 403 TYR cc_start: 0.6423 (m-80) cc_final: 0.6010 (m-80) REVERT: A 471 LYS cc_start: 0.7848 (tmmt) cc_final: 0.7539 (tttp) REVERT: A 530 PHE cc_start: 0.7974 (t80) cc_final: 0.7068 (t80) REVERT: A 552 LYS cc_start: 0.5303 (OUTLIER) cc_final: 0.5049 (mtmm) REVERT: A 558 MET cc_start: 0.6738 (mpt) cc_final: 0.6489 (mpt) REVERT: A 592 MET cc_start: 0.5368 (mmt) cc_final: 0.5149 (mmt) REVERT: A 875 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8034 (mt) REVERT: B 125 GLN cc_start: 0.7742 (mt0) cc_final: 0.6870 (pt0) outliers start: 40 outliers final: 34 residues processed: 213 average time/residue: 0.2374 time to fit residues: 74.4751 Evaluate side-chains 212 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 175 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 1021 ILE Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12477 Z= 0.269 Angle : 0.637 12.504 16913 Z= 0.343 Chirality : 0.045 0.223 1845 Planarity : 0.004 0.049 2077 Dihedral : 13.918 176.004 1929 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.60 % Favored : 90.26 % Rotamer: Outliers : 3.96 % Allowed : 15.23 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.22), residues: 1399 helix: 1.20 (0.22), residues: 571 sheet: -1.31 (0.43), residues: 131 loop : -2.44 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 534 HIS 0.018 0.002 HIS A 720 PHE 0.050 0.002 PHE A1027 TYR 0.020 0.002 TYR A1185 ARG 0.009 0.001 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 184 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.7363 (t70) cc_final: 0.7153 (t-90) REVERT: A 107 LYS cc_start: 0.7774 (tptm) cc_final: 0.7466 (ttpt) REVERT: A 268 GLN cc_start: 0.6656 (mm-40) cc_final: 0.5259 (mm-40) REVERT: A 278 LYS cc_start: 0.8212 (mttp) cc_final: 0.7517 (mtpp) REVERT: A 333 SER cc_start: 0.8614 (p) cc_final: 0.8325 (t) REVERT: A 368 ASP cc_start: 0.6003 (OUTLIER) cc_final: 0.5484 (m-30) REVERT: A 401 GLN cc_start: 0.7608 (tm-30) cc_final: 0.7246 (tt0) REVERT: A 403 TYR cc_start: 0.6401 (m-80) cc_final: 0.5935 (m-80) REVERT: A 471 LYS cc_start: 0.7954 (tmmt) cc_final: 0.7635 (tttp) REVERT: A 496 ILE cc_start: 0.5999 (OUTLIER) cc_final: 0.5650 (mm) REVERT: A 552 LYS cc_start: 0.5691 (OUTLIER) cc_final: 0.5365 (mtmm) REVERT: A 558 MET cc_start: 0.6787 (mpt) cc_final: 0.6532 (mpt) REVERT: A 592 MET cc_start: 0.5373 (mmt) cc_final: 0.5127 (mmt) REVERT: A 875 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8082 (tp) outliers start: 50 outliers final: 44 residues processed: 221 average time/residue: 0.2298 time to fit residues: 74.5605 Evaluate side-chains 225 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 177 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 1021 ILE Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 115 optimal weight: 0.0370 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 0.4980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN B 163 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12477 Z= 0.177 Angle : 0.588 10.836 16913 Z= 0.317 Chirality : 0.043 0.205 1845 Planarity : 0.004 0.050 2077 Dihedral : 13.824 178.384 1929 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.24 % Favored : 91.62 % Rotamer: Outliers : 3.34 % Allowed : 15.85 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.23), residues: 1399 helix: 1.36 (0.22), residues: 573 sheet: -1.02 (0.45), residues: 125 loop : -2.36 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 362 HIS 0.009 0.001 HIS A 720 PHE 0.058 0.001 PHE A1027 TYR 0.015 0.001 TYR A 237 ARG 0.009 0.001 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.7401 (t70) cc_final: 0.7151 (t-90) REVERT: A 107 LYS cc_start: 0.7762 (tptm) cc_final: 0.7492 (ttpt) REVERT: A 268 GLN cc_start: 0.6553 (mm-40) cc_final: 0.5525 (mt0) REVERT: A 278 LYS cc_start: 0.8202 (mttp) cc_final: 0.7548 (mtpp) REVERT: A 333 SER cc_start: 0.8487 (p) cc_final: 0.8286 (t) REVERT: A 386 ARG cc_start: 0.6209 (ttp-110) cc_final: 0.5786 (mtm-85) REVERT: A 401 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7230 (tt0) REVERT: A 403 TYR cc_start: 0.6298 (m-80) cc_final: 0.5826 (m-80) REVERT: A 471 LYS cc_start: 0.7726 (tmmt) cc_final: 0.7396 (tttp) REVERT: A 496 ILE cc_start: 0.5593 (OUTLIER) cc_final: 0.5367 (mm) REVERT: A 530 PHE cc_start: 0.8017 (t80) cc_final: 0.7121 (t80) REVERT: A 552 LYS cc_start: 0.5243 (OUTLIER) cc_final: 0.5000 (mtmm) REVERT: A 558 MET cc_start: 0.6754 (mpt) cc_final: 0.6524 (mpt) REVERT: A 592 MET cc_start: 0.5378 (mmt) cc_final: 0.5116 (mmt) REVERT: A 875 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8043 (mt) REVERT: A 1050 LYS cc_start: 0.7178 (mmtt) cc_final: 0.6956 (mmtt) REVERT: C 137 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6476 (t0) outliers start: 42 outliers final: 34 residues processed: 209 average time/residue: 0.2330 time to fit residues: 73.5938 Evaluate side-chains 212 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 174 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 1021 ILE Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 0.4980 chunk 141 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 chunk 69 optimal weight: 0.0070 chunk 89 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN C 193 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12477 Z= 0.163 Angle : 0.584 9.779 16913 Z= 0.313 Chirality : 0.042 0.205 1845 Planarity : 0.004 0.050 2077 Dihedral : 13.772 178.427 1929 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.38 % Favored : 91.48 % Rotamer: Outliers : 2.56 % Allowed : 16.78 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1399 helix: 1.41 (0.22), residues: 574 sheet: -1.16 (0.41), residues: 145 loop : -2.32 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 362 HIS 0.007 0.001 HIS A 720 PHE 0.051 0.001 PHE A1027 TYR 0.016 0.001 TYR A 237 ARG 0.009 0.000 ARG B 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.7442 (t70) cc_final: 0.7180 (t-90) REVERT: A 107 LYS cc_start: 0.7860 (tptm) cc_final: 0.7522 (ttpt) REVERT: A 268 GLN cc_start: 0.6415 (mm-40) cc_final: 0.5815 (mm-40) REVERT: A 278 LYS cc_start: 0.8194 (mttp) cc_final: 0.7578 (mtpp) REVERT: A 333 SER cc_start: 0.8490 (p) cc_final: 0.8264 (t) REVERT: A 386 ARG cc_start: 0.6165 (ttp-110) cc_final: 0.5791 (mtm-85) REVERT: A 401 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7146 (tt0) REVERT: A 403 TYR cc_start: 0.6232 (m-80) cc_final: 0.5704 (m-80) REVERT: A 471 LYS cc_start: 0.7724 (tmmt) cc_final: 0.7398 (tttp) REVERT: A 484 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7248 (pm20) REVERT: A 530 PHE cc_start: 0.7931 (t80) cc_final: 0.7070 (t80) REVERT: A 592 MET cc_start: 0.5321 (mmt) cc_final: 0.5070 (mmt) REVERT: A 875 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8031 (mt) REVERT: A 1023 ASP cc_start: 0.7500 (m-30) cc_final: 0.7265 (m-30) REVERT: A 1050 LYS cc_start: 0.7185 (mmtt) cc_final: 0.6969 (mmtt) REVERT: A 1098 LEU cc_start: 0.7970 (tp) cc_final: 0.7599 (tt) REVERT: A 1133 LEU cc_start: 0.8588 (tp) cc_final: 0.8335 (tp) REVERT: B 137 ASP cc_start: 0.8193 (m-30) cc_final: 0.7894 (m-30) REVERT: C 137 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6560 (t0) REVERT: C 219 GLU cc_start: 0.6967 (pm20) cc_final: 0.6503 (tp30) outliers start: 32 outliers final: 23 residues processed: 206 average time/residue: 0.2192 time to fit residues: 67.4073 Evaluate side-chains 202 residues out of total 1289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.0040 chunk 112 optimal weight: 0.0370 chunk 47 optimal weight: 4.9990 chunk 115 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 overall best weight: 0.8072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.203177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.171583 restraints weight = 19582.271| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 3.53 r_work: 0.3639 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12477 Z= 0.197 Angle : 0.599 11.174 16913 Z= 0.319 Chirality : 0.043 0.250 1845 Planarity : 0.004 0.048 2077 Dihedral : 13.770 177.192 1929 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.81 % Favored : 91.05 % Rotamer: Outliers : 2.56 % Allowed : 17.25 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.23), residues: 1399 helix: 1.45 (0.22), residues: 574 sheet: -1.13 (0.41), residues: 145 loop : -2.28 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1193 HIS 0.012 0.001 HIS A 720 PHE 0.049 0.001 PHE A1027 TYR 0.018 0.001 TYR A1036 ARG 0.008 0.001 ARG B 230 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2861.76 seconds wall clock time: 52 minutes 36.41 seconds (3156.41 seconds total)