Starting phenix.real_space_refine on Thu Feb 15 13:48:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgh_31969/02_2024/7vgh_31969_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgh_31969/02_2024/7vgh_31969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgh_31969/02_2024/7vgh_31969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgh_31969/02_2024/7vgh_31969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgh_31969/02_2024/7vgh_31969_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgh_31969/02_2024/7vgh_31969_updated.pdb" } resolution = 3.39 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 7976 2.51 5 N 2084 2.21 5 O 2285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 437": "NH1" <-> "NH2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B ARG 525": "NH1" <-> "NH2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B ARG 572": "NH1" <-> "NH2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B ARG 602": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 631": "NH1" <-> "NH2" Residue "B GLU 662": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 707": "OE1" <-> "OE2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "B GLU 788": "OE1" <-> "OE2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 832": "NH1" <-> "NH2" Residue "B ARG 841": "NH1" <-> "NH2" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B ARG 882": "NH1" <-> "NH2" Residue "B ARG 930": "NH1" <-> "NH2" Residue "B ARG 941": "NH1" <-> "NH2" Residue "B ARG 946": "NH1" <-> "NH2" Residue "B ARG 952": "NH1" <-> "NH2" Residue "B ARG 1032": "NH1" <-> "NH2" Residue "B ARG 1182": "NH1" <-> "NH2" Residue "B ARG 1206": "NH1" <-> "NH2" Residue "B ARG 1225": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12404 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2654 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 30, 'TRANS': 307} Chain: "B" Number of atoms: 9584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9584 Classifications: {'peptide': 1183} Link IDs: {'PTRANS': 32, 'TRANS': 1150} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.83, per 1000 atoms: 0.55 Number of scatterers: 12404 At special positions: 0 Unit cell: (99.882, 107.4, 173.988, 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 57 16.00 P 1 15.00 Mg 1 11.99 O 2285 8.00 N 2084 7.00 C 7976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 162 " distance=2.04 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 Links applied ALPHA1-3 " MAN C 3 " - " MAN C 4 " " MAN D 3 " - " MAN D 6 " ALPHA1-4 " NAG C 2 " - " MAN C 3 " " NAG D 2 " - " MAN D 3 " ALPHA1-6 " MAN D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A 401 " - " ASN A 286 " " NAG C 1 " - " ASN B 368 " " NAG D 1 " - " ASN A 171 " " NAG E 1 " - " ASN A 75 " Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.1 seconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2854 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 9 sheets defined 36.2% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 32 through 56 removed outlier: 3.946A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Proline residue: A 37 - end of helix removed outlier: 3.833A pdb=" N GLY A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 122 through 125 No H-bonds generated for 'chain 'A' and resid 122 through 125' Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 164 through 167 No H-bonds generated for 'chain 'A' and resid 164 through 167' Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 248 through 254 Processing helix chain 'A' and resid 316 through 341 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 107 through 117 removed outlier: 3.773A pdb=" N LYS B 117 " --> pdb=" O PHE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 removed outlier: 3.697A pdb=" N ALA B 132 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 174 removed outlier: 3.885A pdb=" N THR B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS B 171 " --> pdb=" O HIS B 167 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE B 173 " --> pdb=" O MET B 169 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 193 No H-bonds generated for 'chain 'B' and resid 191 through 193' Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 244 through 247 No H-bonds generated for 'chain 'B' and resid 244 through 247' Processing helix chain 'B' and resid 253 through 256 No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 334 through 363 removed outlier: 3.785A pdb=" N TYR B 339 " --> pdb=" O TYR B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 381 through 398 removed outlier: 3.866A pdb=" N TRP B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 421 removed outlier: 3.582A pdb=" N ASN B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 425 No H-bonds generated for 'chain 'B' and resid 423 through 425' Processing helix chain 'B' and resid 443 through 446 removed outlier: 3.637A pdb=" N GLY B 446 " --> pdb=" O GLU B 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 443 through 446' Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 522 through 525 No H-bonds generated for 'chain 'B' and resid 522 through 525' Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.587A pdb=" N LEU B 531 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 532 " --> pdb=" O PHE B 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 527 through 532' Processing helix chain 'B' and resid 553 through 565 removed outlier: 3.860A pdb=" N ALA B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 622 through 627 removed outlier: 5.071A pdb=" N GLU B 627 " --> pdb=" O THR B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 648 removed outlier: 4.417A pdb=" N GLN B 637 " --> pdb=" O PRO B 634 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU B 638 " --> pdb=" O THR B 635 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 639 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 640 " --> pdb=" O GLN B 637 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP B 641 " --> pdb=" O GLU B 638 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP B 644 " --> pdb=" O ASP B 641 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 645 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 646 " --> pdb=" O LEU B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 677 removed outlier: 3.857A pdb=" N TRP B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 738 through 745 removed outlier: 3.642A pdb=" N ILE B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY B 743 " --> pdb=" O ALA B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 770 removed outlier: 3.635A pdb=" N SER B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 817 through 819 No H-bonds generated for 'chain 'B' and resid 817 through 819' Processing helix chain 'B' and resid 842 through 845 No H-bonds generated for 'chain 'B' and resid 842 through 845' Processing helix chain 'B' and resid 849 through 859 removed outlier: 4.148A pdb=" N GLU B 859 " --> pdb=" O ASP B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 882 removed outlier: 3.838A pdb=" N ALA B 874 " --> pdb=" O PRO B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 903 Processing helix chain 'B' and resid 929 through 937 removed outlier: 3.807A pdb=" N LEU B 935 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 936 " --> pdb=" O GLN B 933 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B 937 " --> pdb=" O ARG B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 957 removed outlier: 3.728A pdb=" N PHE B 955 " --> pdb=" O LEU B 951 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR B 956 " --> pdb=" O ARG B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 971 removed outlier: 4.889A pdb=" N VAL B 964 " --> pdb=" O ALA B 960 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N HIS B 965 " --> pdb=" O PHE B 961 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE B 966 " --> pdb=" O THR B 962 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 970 " --> pdb=" O PHE B 966 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE B 971 " --> pdb=" O TRP B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 985 No H-bonds generated for 'chain 'B' and resid 982 through 985' Processing helix chain 'B' and resid 995 through 1003 Processing helix chain 'B' and resid 1016 through 1023 removed outlier: 3.754A pdb=" N VAL B1021 " --> pdb=" O LEU B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1055 removed outlier: 3.597A pdb=" N PHE B1034 " --> pdb=" O TYR B1030 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B1035 " --> pdb=" O LYS B1031 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B1050 " --> pdb=" O ILE B1046 " (cutoff:3.500A) Proline residue: B1051 - end of helix Processing helix chain 'B' and resid 1069 through 1078 Processing helix chain 'B' and resid 1083 through 1087 Processing helix chain 'B' and resid 1097 through 1117 removed outlier: 3.857A pdb=" N ASP B1116 " --> pdb=" O GLY B1112 " (cutoff:3.500A) Processing helix chain 'B' and resid 1136 through 1139 No H-bonds generated for 'chain 'B' and resid 1136 through 1139' Processing helix chain 'B' and resid 1143 through 1167 removed outlier: 3.788A pdb=" N LEU B1151 " --> pdb=" O LEU B1147 " (cutoff:3.500A) Proline residue: B1159 - end of helix Processing helix chain 'B' and resid 1174 through 1180 Processing helix chain 'B' and resid 1218 through 1222 Processing sheet with id= A, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.797A pdb=" N HIS A 299 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 115 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 108 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR A 112 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU A 265 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU A 114 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ARG A 263 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 95 through 100 removed outlier: 4.560A pdb=" N ALA A 282 " --> pdb=" O GLN A 179 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 178 through 181 Processing sheet with id= D, first strand: chain 'B' and resid 199 through 203 removed outlier: 3.963A pdb=" N SER B 216 " --> pdb=" O HIS B 307 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 309 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU B 214 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 238 through 241 removed outlier: 4.037A pdb=" N TYR B 225 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 277 through 279 removed outlier: 4.083A pdb=" N GLY B 277 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 906 through 908 removed outlier: 6.283A pdb=" N TYR B 450 " --> pdb=" O LEU B 889 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE B 891 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE B 452 " --> pdb=" O ILE B 891 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS B 727 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N SER B 453 " --> pdb=" O LYS B 727 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP B 729 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 863 " --> pdb=" O VAL B 730 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR B 732 " --> pdb=" O VAL B 863 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N CYS B 865 " --> pdb=" O THR B 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 578 through 581 Processing sheet with id= I, first strand: chain 'B' and resid 700 through 706 removed outlier: 6.956A pdb=" N LEU B 656 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA B 703 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 654 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA B 705 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG B 652 " --> pdb=" O ALA B 705 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 592 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG B 608 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL B 590 " --> pdb=" O ARG B 608 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 5.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3944 1.35 - 1.47: 3347 1.47 - 1.60: 5332 1.60 - 1.73: 0 1.73 - 1.85: 86 Bond restraints: 12709 Sorted by residual: bond pdb=" C1 MAN D 6 " pdb=" C2 MAN D 6 " ideal model delta sigma weight residual 1.526 1.580 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" CA ILE B 661 " pdb=" C ILE B 661 " ideal model delta sigma weight residual 1.522 1.553 -0.031 1.44e-02 4.82e+03 4.68e+00 bond pdb=" C5 MAN D 6 " pdb=" O5 MAN D 6 " ideal model delta sigma weight residual 1.418 1.460 -0.042 2.00e-02 2.50e+03 4.35e+00 bond pdb=" C1 MAN D 5 " pdb=" C2 MAN D 5 " ideal model delta sigma weight residual 1.526 1.567 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C5 MAN C 3 " pdb=" O5 MAN C 3 " ideal model delta sigma weight residual 1.418 1.458 -0.040 2.00e-02 2.50e+03 3.99e+00 ... (remaining 12704 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.39: 180 104.39 - 111.80: 5783 111.80 - 119.20: 4432 119.20 - 126.61: 6653 126.61 - 134.02: 191 Bond angle restraints: 17239 Sorted by residual: angle pdb=" C GLU B 662 " pdb=" CA GLU B 662 " pdb=" CB GLU B 662 " ideal model delta sigma weight residual 117.23 108.75 8.48 1.36e+00 5.41e-01 3.89e+01 angle pdb=" N THR B 465 " pdb=" CA THR B 465 " pdb=" C THR B 465 " ideal model delta sigma weight residual 111.02 116.13 -5.11 1.25e+00 6.40e-01 1.67e+01 angle pdb=" N VAL B 624 " pdb=" CA VAL B 624 " pdb=" C VAL B 624 " ideal model delta sigma weight residual 112.96 108.96 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" CA GLU B 662 " pdb=" C GLU B 662 " pdb=" N GLU B 663 " ideal model delta sigma weight residual 119.98 116.81 3.17 8.50e-01 1.38e+00 1.39e+01 angle pdb=" N ARG B 600 " pdb=" CA ARG B 600 " pdb=" C ARG B 600 " ideal model delta sigma weight residual 112.04 106.72 5.32 1.44e+00 4.82e-01 1.37e+01 ... (remaining 17234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.72: 7158 24.72 - 49.43: 435 49.43 - 74.15: 47 74.15 - 98.87: 34 98.87 - 123.59: 17 Dihedral angle restraints: 7691 sinusoidal: 3244 harmonic: 4447 Sorted by residual: dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 92 " pdb=" CB CYS A 92 " ideal model delta sinusoidal sigma weight residual 93.00 36.85 56.15 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CA ARG B 572 " pdb=" C ARG B 572 " pdb=" N THR B 573 " pdb=" CA THR B 573 " ideal model delta harmonic sigma weight residual 180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ASP B 478 " pdb=" C ASP B 478 " pdb=" N HIS B 479 " pdb=" CA HIS B 479 " ideal model delta harmonic sigma weight residual 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 7688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1739 0.081 - 0.162: 171 0.162 - 0.243: 10 0.243 - 0.324: 0 0.324 - 0.405: 1 Chirality restraints: 1921 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 75 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CB ILE B 136 " pdb=" CA ILE B 136 " pdb=" CG1 ILE B 136 " pdb=" CG2 ILE B 136 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CG LEU B1037 " pdb=" CB LEU B1037 " pdb=" CD1 LEU B1037 " pdb=" CD2 LEU B1037 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1918 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 959 " 0.019 2.00e-02 2.50e+03 2.11e-02 7.81e+00 pdb=" CG PHE B 959 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 959 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE B 959 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 959 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 959 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 959 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 160 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 161 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1191 " -0.021 2.00e-02 2.50e+03 1.46e-02 5.36e+00 pdb=" CG TRP B1191 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B1191 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B1191 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1191 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B1191 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1191 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1191 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1191 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B1191 " -0.001 2.00e-02 2.50e+03 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 105 2.57 - 3.15: 10366 3.15 - 3.74: 17898 3.74 - 4.32: 25388 4.32 - 4.90: 41940 Nonbonded interactions: 95697 Sorted by model distance: nonbonded pdb=" OD2 PHD B 454 " pdb="MG MG B1401 " model vdw 1.989 2.170 nonbonded pdb=" O THR B 456 " pdb="MG MG B1401 " model vdw 2.094 2.170 nonbonded pdb=" NH1 ARG B 946 " pdb=" O ASP B1004 " model vdw 2.217 2.520 nonbonded pdb=" O PRO A 279 " pdb=" OH TYR A 283 " model vdw 2.231 2.440 nonbonded pdb=" O PHE A 220 " pdb=" OG1 THR A 223 " model vdw 2.238 2.440 ... (remaining 95692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 3.770 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 35.540 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 0.054 12709 Z= 0.321 Angle : 0.750 10.477 17239 Z= 0.407 Chirality : 0.048 0.405 1921 Planarity : 0.004 0.067 2184 Dihedral : 17.585 123.585 4828 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 0.23 % Allowed : 0.53 % Favored : 99.24 % 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: -2.72 (0.21), residues: 1512 helix: -0.52 (0.22), residues: 549 sheet: -0.74 (0.40), residues: 173 loop : -3.16 (0.19), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1191 HIS 0.007 0.001 HIS B1213 PHE 0.047 0.002 PHE B 959 TYR 0.037 0.002 TYR A 65 ARG 0.007 0.001 ARG B 835 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 1.516 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 120 average time/residue: 0.2853 time to fit residues: 48.3007 Evaluate side-chains 97 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 662 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12709 Z= 0.159 Angle : 0.612 10.822 17239 Z= 0.306 Chirality : 0.044 0.291 1921 Planarity : 0.004 0.049 2184 Dihedral : 13.536 124.403 1946 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 0.69 % Allowed : 8.63 % Favored : 90.69 % 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: -2.32 (0.21), residues: 1512 helix: -0.05 (0.23), residues: 540 sheet: -0.61 (0.40), residues: 169 loop : -2.96 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 96 HIS 0.006 0.001 HIS B 359 PHE 0.021 0.001 PHE B 959 TYR 0.014 0.001 TYR B 123 ARG 0.005 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.564 Fit side-chains REVERT: A 65 TYR cc_start: 0.7602 (t80) cc_final: 0.7392 (t80) REVERT: A 280 ARG cc_start: 0.7972 (ptt90) cc_final: 0.7193 (ttp80) REVERT: B 709 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7432 (tptm) REVERT: B 769 MET cc_start: 0.7443 (tmm) cc_final: 0.6893 (tmm) REVERT: B 1057 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7482 (mm-40) outliers start: 9 outliers final: 6 residues processed: 118 average time/residue: 0.2942 time to fit residues: 49.5140 Evaluate side-chains 105 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 148 optimal weight: 0.0270 chunk 122 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 110 optimal weight: 0.0570 overall best weight: 1.1158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 131 GLN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 ASN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 HIS B1196 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12709 Z= 0.165 Angle : 0.583 10.066 17239 Z= 0.291 Chirality : 0.042 0.281 1921 Planarity : 0.004 0.048 2184 Dihedral : 11.902 126.285 1943 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 1.15 % Allowed : 12.44 % Favored : 86.41 % 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: -2.09 (0.21), residues: 1512 helix: 0.15 (0.23), residues: 547 sheet: -0.39 (0.39), residues: 174 loop : -2.89 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 96 HIS 0.005 0.001 HIS B 359 PHE 0.017 0.001 PHE B 959 TYR 0.013 0.001 TYR A 111 ARG 0.005 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 1.367 Fit side-chains REVERT: A 65 TYR cc_start: 0.7647 (t80) cc_final: 0.6828 (t80) REVERT: B 94 ASN cc_start: 0.7543 (t0) cc_final: 0.7183 (p0) REVERT: B 105 PHE cc_start: 0.8289 (p90) cc_final: 0.7992 (p90) REVERT: B 115 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: B 632 MET cc_start: 0.7490 (tpp) cc_final: 0.7018 (ppp) REVERT: B 709 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7354 (tptm) REVERT: B 1062 ASP cc_start: 0.6147 (t0) cc_final: 0.5800 (t0) outliers start: 15 outliers final: 9 residues processed: 114 average time/residue: 0.2788 time to fit residues: 45.2623 Evaluate side-chains 106 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 0.0670 chunk 15 optimal weight: 0.0030 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 ASN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12709 Z= 0.181 Angle : 0.587 10.268 17239 Z= 0.290 Chirality : 0.042 0.282 1921 Planarity : 0.004 0.046 2184 Dihedral : 10.918 125.360 1943 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 1.53 % Allowed : 13.66 % Favored : 84.81 % 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: -2.02 (0.21), residues: 1512 helix: 0.20 (0.23), residues: 549 sheet: -0.33 (0.39), residues: 175 loop : -2.86 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 96 HIS 0.005 0.001 HIS B 359 PHE 0.016 0.001 PHE B 959 TYR 0.014 0.001 TYR B 123 ARG 0.005 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.482 Fit side-chains REVERT: A 65 TYR cc_start: 0.7714 (t80) cc_final: 0.6910 (t80) REVERT: B 94 ASN cc_start: 0.7629 (t0) cc_final: 0.7350 (p0) REVERT: B 105 PHE cc_start: 0.8295 (p90) cc_final: 0.7995 (p90) REVERT: B 709 LYS cc_start: 0.7913 (mmmt) cc_final: 0.7331 (tptm) REVERT: B 1104 PHE cc_start: 0.7952 (m-10) cc_final: 0.7618 (m-10) outliers start: 20 outliers final: 14 residues processed: 111 average time/residue: 0.2748 time to fit residues: 44.2505 Evaluate side-chains 107 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12709 Z= 0.218 Angle : 0.592 10.250 17239 Z= 0.295 Chirality : 0.043 0.302 1921 Planarity : 0.004 0.045 2184 Dihedral : 9.717 117.119 1943 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 1.60 % Allowed : 14.81 % Favored : 83.59 % 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: -1.97 (0.21), residues: 1512 helix: 0.25 (0.23), residues: 550 sheet: -0.22 (0.39), residues: 172 loop : -2.86 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 96 HIS 0.004 0.001 HIS B 359 PHE 0.021 0.001 PHE B 959 TYR 0.016 0.001 TYR B 123 ARG 0.005 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.568 Fit side-chains REVERT: A 65 TYR cc_start: 0.7874 (t80) cc_final: 0.7078 (t80) REVERT: B 94 ASN cc_start: 0.7672 (t0) cc_final: 0.7381 (p0) REVERT: B 105 PHE cc_start: 0.8364 (p90) cc_final: 0.8077 (p90) REVERT: B 589 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.7202 (p0) REVERT: B 632 MET cc_start: 0.7261 (tpp) cc_final: 0.6924 (ppp) REVERT: B 709 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7352 (tptm) REVERT: B 1057 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7277 (mt0) outliers start: 21 outliers final: 16 residues processed: 116 average time/residue: 0.2770 time to fit residues: 46.8488 Evaluate side-chains 114 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 36 optimal weight: 0.1980 chunk 146 optimal weight: 3.9990 chunk 121 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12709 Z= 0.181 Angle : 0.561 10.142 17239 Z= 0.282 Chirality : 0.042 0.302 1921 Planarity : 0.003 0.046 2184 Dihedral : 9.131 114.520 1943 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 1.91 % Allowed : 15.34 % 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: -1.90 (0.21), residues: 1512 helix: 0.31 (0.23), residues: 552 sheet: -0.23 (0.39), residues: 175 loop : -2.82 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1191 HIS 0.005 0.001 HIS B 359 PHE 0.017 0.001 PHE B 345 TYR 0.014 0.001 TYR B 123 ARG 0.007 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.802 Fit side-chains REVERT: A 65 TYR cc_start: 0.7823 (t80) cc_final: 0.7204 (t80) REVERT: B 94 ASN cc_start: 0.7732 (t0) cc_final: 0.7394 (p0) REVERT: B 105 PHE cc_start: 0.8325 (p90) cc_final: 0.7999 (p90) REVERT: B 709 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7224 (tptm) REVERT: B 1057 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7170 (mt0) outliers start: 25 outliers final: 17 residues processed: 120 average time/residue: 0.2819 time to fit residues: 48.9870 Evaluate side-chains 114 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 145 optimal weight: 0.0010 chunk 91 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12709 Z= 0.155 Angle : 0.544 10.126 17239 Z= 0.273 Chirality : 0.041 0.300 1921 Planarity : 0.003 0.046 2184 Dihedral : 8.684 109.884 1943 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 2.06 % Allowed : 15.80 % Favored : 82.14 % 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: -1.82 (0.21), residues: 1512 helix: 0.43 (0.24), residues: 549 sheet: -0.26 (0.39), residues: 177 loop : -2.80 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1191 HIS 0.005 0.001 HIS B 359 PHE 0.015 0.001 PHE B 345 TYR 0.013 0.001 TYR A 111 ARG 0.006 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.552 Fit side-chains REVERT: A 65 TYR cc_start: 0.7866 (t80) cc_final: 0.7297 (t80) REVERT: A 104 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.5246 (m-80) REVERT: B 94 ASN cc_start: 0.7725 (t0) cc_final: 0.7386 (p0) REVERT: B 589 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7174 (p0) REVERT: B 673 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.5538 (p90) REVERT: B 709 LYS cc_start: 0.7680 (mmmt) cc_final: 0.7270 (tptm) REVERT: B 1057 GLN cc_start: 0.7534 (mm-40) cc_final: 0.7081 (mt0) outliers start: 27 outliers final: 17 residues processed: 120 average time/residue: 0.2857 time to fit residues: 50.2095 Evaluate side-chains 117 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 673 PHE Chi-restraints excluded: chain B residue 752 ASP Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 0.0670 chunk 13 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12709 Z= 0.182 Angle : 0.554 10.246 17239 Z= 0.280 Chirality : 0.042 0.301 1921 Planarity : 0.003 0.045 2184 Dihedral : 8.560 108.072 1943 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 1.83 % Allowed : 16.56 % Favored : 81.60 % 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 (0.21), residues: 1512 helix: 0.44 (0.23), residues: 551 sheet: -0.25 (0.39), residues: 174 loop : -2.78 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1191 HIS 0.004 0.001 HIS B 359 PHE 0.015 0.001 PHE B 959 TYR 0.014 0.001 TYR B 123 ARG 0.006 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.432 Fit side-chains REVERT: A 65 TYR cc_start: 0.7872 (t80) cc_final: 0.7268 (t80) REVERT: A 104 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.5242 (m-80) REVERT: B 94 ASN cc_start: 0.7720 (t0) cc_final: 0.7329 (p0) REVERT: B 589 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7171 (p0) REVERT: B 673 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.5630 (p90) REVERT: B 697 ASP cc_start: 0.7093 (m-30) cc_final: 0.6866 (m-30) REVERT: B 709 LYS cc_start: 0.7609 (mmmt) cc_final: 0.7184 (tptm) REVERT: B 834 MET cc_start: 0.3260 (OUTLIER) cc_final: 0.2738 (mmm) outliers start: 24 outliers final: 17 residues processed: 118 average time/residue: 0.2685 time to fit residues: 46.3464 Evaluate side-chains 116 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 673 PHE Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 0.0050 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN ** B1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12709 Z= 0.289 Angle : 0.616 10.981 17239 Z= 0.312 Chirality : 0.044 0.315 1921 Planarity : 0.004 0.046 2184 Dihedral : 8.750 108.274 1943 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 2.06 % Allowed : 16.79 % Favored : 81.15 % 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: -1.97 (0.21), residues: 1512 helix: 0.24 (0.23), residues: 553 sheet: -0.43 (0.39), residues: 173 loop : -2.82 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1191 HIS 0.004 0.001 HIS B 965 PHE 0.023 0.002 PHE B 959 TYR 0.019 0.001 TYR B 123 ARG 0.006 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 1.480 Fit side-chains REVERT: A 65 TYR cc_start: 0.8169 (t80) cc_final: 0.7577 (t80) REVERT: A 104 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.5201 (m-80) REVERT: B 94 ASN cc_start: 0.7763 (t0) cc_final: 0.7372 (p0) REVERT: B 589 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7166 (p0) REVERT: B 652 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.6822 (ptm160) REVERT: B 673 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.5601 (p90) REVERT: B 697 ASP cc_start: 0.7107 (m-30) cc_final: 0.6868 (m-30) REVERT: B 709 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7460 (tptm) REVERT: B 834 MET cc_start: 0.3299 (OUTLIER) cc_final: 0.2782 (mmm) REVERT: B 1057 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7301 (mt0) outliers start: 27 outliers final: 20 residues processed: 113 average time/residue: 0.2787 time to fit residues: 45.4059 Evaluate side-chains 117 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 652 ARG Chi-restraints excluded: chain B residue 673 PHE Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 834 MET Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1084 VAL Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 150 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 ASN ** B1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12709 Z= 0.165 Angle : 0.560 10.323 17239 Z= 0.281 Chirality : 0.042 0.296 1921 Planarity : 0.004 0.046 2184 Dihedral : 8.496 107.455 1943 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 1.45 % Allowed : 17.71 % Favored : 80.84 % 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: -1.86 (0.21), residues: 1512 helix: 0.40 (0.23), residues: 554 sheet: -0.40 (0.39), residues: 174 loop : -2.81 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1191 HIS 0.011 0.001 HIS B 630 PHE 0.018 0.001 PHE B 345 TYR 0.015 0.001 TYR B 123 ARG 0.007 0.000 ARG A 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.409 Fit side-chains REVERT: A 65 TYR cc_start: 0.7967 (t80) cc_final: 0.7400 (t80) REVERT: A 100 LEU cc_start: 0.8387 (mt) cc_final: 0.8026 (mt) REVERT: A 104 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.4973 (m-80) REVERT: B 94 ASN cc_start: 0.7704 (t0) cc_final: 0.7327 (p0) REVERT: B 589 ASN cc_start: 0.7575 (OUTLIER) cc_final: 0.7139 (p0) REVERT: B 652 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7511 (ptm160) REVERT: B 673 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.5647 (p90) REVERT: B 709 LYS cc_start: 0.7667 (mmmt) cc_final: 0.7219 (tptm) REVERT: B 834 MET cc_start: 0.3228 (mmm) cc_final: 0.2706 (mmm) REVERT: B 1057 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7138 (mt0) outliers start: 19 outliers final: 14 residues processed: 113 average time/residue: 0.2737 time to fit residues: 44.5352 Evaluate side-chains 115 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 652 ARG Chi-restraints excluded: chain B residue 673 PHE Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 837 GLN Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 1029 ASN Chi-restraints excluded: chain B residue 1223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 123 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.114657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.078798 restraints weight = 22203.277| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.51 r_work: 0.2735 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12709 Z= 0.321 Angle : 0.628 10.956 17239 Z= 0.318 Chirality : 0.045 0.316 1921 Planarity : 0.004 0.048 2184 Dihedral : 8.745 108.149 1943 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 2.21 % Allowed : 17.02 % Favored : 80.76 % 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: -2.02 (0.21), residues: 1512 helix: 0.22 (0.23), residues: 562 sheet: -0.66 (0.39), residues: 179 loop : -2.84 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1191 HIS 0.007 0.001 HIS B 630 PHE 0.025 0.002 PHE B 959 TYR 0.020 0.001 TYR B 123 ARG 0.007 0.000 ARG A 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2575.76 seconds wall clock time: 47 minutes 43.90 seconds (2863.90 seconds total)