Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 09:59:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byp_16330/04_2023/8byp_16330_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byp_16330/04_2023/8byp_16330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byp_16330/04_2023/8byp_16330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byp_16330/04_2023/8byp_16330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byp_16330/04_2023/8byp_16330_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byp_16330/04_2023/8byp_16330_neut.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.154 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 12730 2.51 5 N 3214 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N GLU 99": "OE1" <-> "OE2" Residue "N GLU 126": "OE1" <-> "OE2" Residue "N GLU 467": "OE1" <-> "OE2" Residue "N GLU 535": "OE1" <-> "OE2" Residue "N GLU 585": "OE1" <-> "OE2" Residue "N GLU 598": "OE1" <-> "OE2" Residue "N GLU 600": "OE1" <-> "OE2" Residue "N GLU 894": "OE1" <-> "OE2" Residue "N PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 976": "OE1" <-> "OE2" Residue "N GLU 982": "OE1" <-> "OE2" Residue "N GLU 1006": "OE1" <-> "OE2" Residue "N TYR 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 1164": "OE1" <-> "OE2" Residue "X GLU 135": "OE1" <-> "OE2" Residue "X PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 197": "OE1" <-> "OE2" Residue "X GLU 386": "OE1" <-> "OE2" Residue "X ARG 425": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 19836 Number of models: 1 Model: "" Number of chains: 2 Chain: "N" Number of atoms: 9554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 9554 Classifications: {'peptide': 1156} Link IDs: {'PTRANS': 37, 'TRANS': 1118} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "X" Number of atoms: 10282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1265, 10282 Classifications: {'peptide': 1265} Link IDs: {'PTRANS': 46, 'TRANS': 1218} Chain breaks: 1 Time building chain proxies: 9.78, per 1000 atoms: 0.49 Number of scatterers: 19836 At special positions: 0 Unit cell: (108.15, 118.65, 168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 3857 8.00 N 3214 7.00 C 12730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS X 423 " - pdb=" SG CYS X 467 " 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: 7.48 Conformation dependent library (CDL) restraints added in 2.7 seconds 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4654 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 33 sheets defined 32.6% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'N' and resid 59 through 63 Processing helix chain 'N' and resid 76 through 97 removed outlier: 4.090A pdb=" N VAL N 97 " --> pdb=" O ARG N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 109 Processing helix chain 'N' and resid 193 through 211 removed outlier: 3.831A pdb=" N GLY N 197 " --> pdb=" O ASP N 193 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS N 201 " --> pdb=" O GLY N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 244 Processing helix chain 'N' and resid 261 through 281 removed outlier: 3.614A pdb=" N LEU N 265 " --> pdb=" O ASN N 261 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU N 268 " --> pdb=" O PHE N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 302 Processing helix chain 'N' and resid 303 through 308 Processing helix chain 'N' and resid 311 through 319 removed outlier: 3.630A pdb=" N PHE N 315 " --> pdb=" O ASN N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 330 through 334 removed outlier: 3.717A pdb=" N TRP N 334 " --> pdb=" O ILE N 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 343 through 347 Processing helix chain 'N' and resid 406 through 411 Processing helix chain 'N' and resid 435 through 442 removed outlier: 3.735A pdb=" N ILE N 439 " --> pdb=" O ASP N 435 " (cutoff:3.500A) Processing helix chain 'N' and resid 475 through 484 removed outlier: 3.871A pdb=" N THR N 484 " --> pdb=" O LEU N 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 499 through 504 removed outlier: 3.765A pdb=" N SER N 504 " --> pdb=" O TYR N 500 " (cutoff:3.500A) Processing helix chain 'N' and resid 515 through 524 removed outlier: 3.957A pdb=" N ASN N 524 " --> pdb=" O GLU N 520 " (cutoff:3.500A) Processing helix chain 'N' and resid 533 through 554 Processing helix chain 'N' and resid 570 through 575 Processing helix chain 'N' and resid 582 through 591 removed outlier: 3.523A pdb=" N LEU N 589 " --> pdb=" O GLU N 585 " (cutoff:3.500A) Processing helix chain 'N' and resid 592 through 596 Processing helix chain 'N' and resid 623 through 654 Processing helix chain 'N' and resid 655 through 666 removed outlier: 3.798A pdb=" N LEU N 661 " --> pdb=" O GLN N 657 " (cutoff:3.500A) Processing helix chain 'N' and resid 667 through 689 removed outlier: 4.015A pdb=" N GLN N 674 " --> pdb=" O ASN N 670 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL N 679 " --> pdb=" O LEU N 675 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS N 682 " --> pdb=" O THR N 678 " (cutoff:3.500A) Processing helix chain 'N' and resid 694 through 739 removed outlier: 3.522A pdb=" N ARG N 700 " --> pdb=" O ASP N 696 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP N 710 " --> pdb=" O ASN N 706 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE N 711 " --> pdb=" O ARG N 707 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG N 714 " --> pdb=" O ASP N 710 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE N 715 " --> pdb=" O ILE N 711 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL N 739 " --> pdb=" O PHE N 735 " (cutoff:3.500A) Processing helix chain 'N' and resid 739 through 763 removed outlier: 3.634A pdb=" N ASN N 746 " --> pdb=" O LEU N 742 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS N 753 " --> pdb=" O ASN N 749 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU N 759 " --> pdb=" O ASN N 755 " (cutoff:3.500A) Processing helix chain 'N' and resid 768 through 775 removed outlier: 3.533A pdb=" N GLN N 772 " --> pdb=" O LEU N 768 " (cutoff:3.500A) Processing helix chain 'N' and resid 775 through 780 removed outlier: 3.521A pdb=" N TYR N 780 " --> pdb=" O LEU N 776 " (cutoff:3.500A) Processing helix chain 'N' and resid 784 through 788 Processing helix chain 'N' and resid 792 through 801 removed outlier: 3.814A pdb=" N PHE N 796 " --> pdb=" O ASN N 792 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS N 798 " --> pdb=" O SER N 794 " (cutoff:3.500A) Processing helix chain 'N' and resid 1003 through 1014 removed outlier: 3.583A pdb=" N ALA N1014 " --> pdb=" O ARG N1010 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 33 Processing helix chain 'X' and resid 84 through 105 removed outlier: 4.181A pdb=" N LYS X 105 " --> pdb=" O ARG X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 118 Processing helix chain 'X' and resid 171 through 177 removed outlier: 3.771A pdb=" N ILE X 175 " --> pdb=" O TYR X 171 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER X 176 " --> pdb=" O SER X 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 220 through 237 removed outlier: 3.904A pdb=" N GLU X 228 " --> pdb=" O THR X 224 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL X 230 " --> pdb=" O MET X 226 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS X 231 " --> pdb=" O HIS X 227 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 271 Processing helix chain 'X' and resid 272 through 301 removed outlier: 3.600A pdb=" N LYS X 276 " --> pdb=" O GLY X 272 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA X 277 " --> pdb=" O ILE X 273 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE X 278 " --> pdb=" O ASP X 274 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SER X 280 " --> pdb=" O LYS X 276 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU X 281 " --> pdb=" O ALA X 277 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN X 292 " --> pdb=" O GLU X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 302 through 305 removed outlier: 3.670A pdb=" N VAL X 305 " --> pdb=" O LEU X 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 302 through 305' Processing helix chain 'X' and resid 309 through 319 Processing helix chain 'X' and resid 331 through 344 Processing helix chain 'X' and resid 347 through 355 Processing helix chain 'X' and resid 473 through 475 No H-bonds generated for 'chain 'X' and resid 473 through 475' Processing helix chain 'X' and resid 559 through 567 removed outlier: 3.559A pdb=" N GLN X 567 " --> pdb=" O PHE X 563 " (cutoff:3.500A) Processing helix chain 'X' and resid 585 through 592 Processing helix chain 'X' and resid 602 through 608 removed outlier: 3.596A pdb=" N THR X 606 " --> pdb=" O ASN X 602 " (cutoff:3.500A) Processing helix chain 'X' and resid 618 through 635 removed outlier: 3.916A pdb=" N LEU X 624 " --> pdb=" O PHE X 620 " (cutoff:3.500A) Processing helix chain 'X' and resid 653 through 658 Processing helix chain 'X' and resid 669 through 676 removed outlier: 3.514A pdb=" N GLU X 674 " --> pdb=" O VAL X 670 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 738 removed outlier: 3.868A pdb=" N ALA X 710 " --> pdb=" O GLU X 706 " (cutoff:3.500A) Processing helix chain 'X' and resid 738 through 770 Processing helix chain 'X' and resid 777 through 819 removed outlier: 4.142A pdb=" N ILE X 781 " --> pdb=" O ASP X 777 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS X 809 " --> pdb=" O LYS X 805 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU X 810 " --> pdb=" O PHE X 806 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET X 819 " --> pdb=" O LEU X 815 " (cutoff:3.500A) Processing helix chain 'X' and resid 819 through 844 removed outlier: 3.619A pdb=" N VAL X 823 " --> pdb=" O MET X 819 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP X 825 " --> pdb=" O PRO X 821 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN X 826 " --> pdb=" O LYS X 822 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU X 844 " --> pdb=" O LYS X 840 " (cutoff:3.500A) Processing helix chain 'X' and resid 845 through 850 Processing helix chain 'X' and resid 850 through 865 Processing helix chain 'X' and resid 879 through 886 removed outlier: 4.374A pdb=" N ASN X 886 " --> pdb=" O ASP X 882 " (cutoff:3.500A) Processing helix chain 'X' and resid 886 through 892 Processing helix chain 'X' and resid 1091 through 1102 removed outlier: 3.631A pdb=" N TYR X1102 " --> pdb=" O LEU X1098 " (cutoff:3.500A) Processing helix chain 'X' and resid 1274 through 1280 removed outlier: 3.745A pdb=" N PHE X1278 " --> pdb=" O SER X1274 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN X1279 " --> pdb=" O ALA X1275 " (cutoff:3.500A) Processing helix chain 'X' and resid 1281 through 1284 Processing helix chain 'X' and resid 1287 through 1292 Processing sheet with id=AA1, first strand: chain 'N' and resid 18 through 22 removed outlier: 6.973A pdb=" N ILE N 44 " --> pdb=" O ILE N 40 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP N 45 " --> pdb=" O LEU N 147 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN N 158 " --> pdb=" O CYS N 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 125 through 126 removed outlier: 4.604A pdb=" N LYS N 125 " --> pdb=" O PHE N 141 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE N 141 " --> pdb=" O LYS N 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'N' and resid 183 through 184 removed outlier: 3.985A pdb=" N LYS N 363 " --> pdb=" O LYS N 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 219 through 224 removed outlier: 6.704A pdb=" N SER N 234 " --> pdb=" O TYR N 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 348 through 349 Processing sheet with id=AA6, first strand: chain 'N' and resid 390 through 394 removed outlier: 4.596A pdb=" N LEU N 390 " --> pdb=" O ASN N 385 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE N 469 " --> pdb=" O ILE N 380 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR N 382 " --> pdb=" O ILE N 469 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 494 through 496 removed outlier: 6.338A pdb=" N LYS N 494 " --> pdb=" O VAL N 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'N' and resid 555 through 556 Processing sheet with id=AA9, first strand: chain 'N' and resid 815 through 817 removed outlier: 5.386A pdb=" N LEU N 992 " --> pdb=" O LYS N 888 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS N 888 " --> pdb=" O LEU N 992 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA N 994 " --> pdb=" O TRP N 886 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TRP N 886 " --> pdb=" O ALA N 994 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 847 through 850 removed outlier: 3.990A pdb=" N ARG N 847 " --> pdb=" O LYS N 858 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N VAL N 855 " --> pdb=" O ALA N 994 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA N 994 " --> pdb=" O VAL N 855 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU N 992 " --> pdb=" O LYS N 888 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS N 888 " --> pdb=" O LEU N 992 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA N 994 " --> pdb=" O TRP N 886 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TRP N 886 " --> pdb=" O ALA N 994 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 820 through 824 removed outlier: 3.593A pdb=" N PHE N 831 " --> pdb=" O SER N 820 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 841 through 842 removed outlier: 6.500A pdb=" N LEU N 910 " --> pdb=" O LEU N 898 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN N 900 " --> pdb=" O TRP N 908 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TRP N 908 " --> pdb=" O ASN N 900 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 1036 through 1037 Processing sheet with id=AB5, first strand: chain 'N' and resid 1047 through 1049 removed outlier: 6.321A pdb=" N ILE N1057 " --> pdb=" O ILE N1153 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE N1134 " --> pdb=" O LEU N1141 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N LEU N1143 " --> pdb=" O LEU N1132 " (cutoff:3.500A) removed outlier: 15.086A pdb=" N LEU N1132 " --> pdb=" O LEU N1143 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER N1131 " --> pdb=" O ASN N1125 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASN N1125 " --> pdb=" O SER N1131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 1100 through 1101 Processing sheet with id=AB7, first strand: chain 'N' and resid 1160 through 1161 Processing sheet with id=AB8, first strand: chain 'X' and resid 144 through 150 removed outlier: 4.913A pdb=" N ILE X 145 " --> pdb=" O GLU X 141 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU X 141 " --> pdb=" O ILE X 145 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA X 138 " --> pdb=" O ARG X 23 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N THR X 21 " --> pdb=" O GLN X 140 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLN X 42 " --> pdb=" O ILE X 49 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE X 49 " --> pdb=" O GLN X 42 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP X 48 " --> pdb=" O ILE X 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 123 through 125 Processing sheet with id=AC1, first strand: chain 'X' and resid 191 through 192 Processing sheet with id=AC2, first strand: chain 'X' and resid 195 through 196 Processing sheet with id=AC3, first strand: chain 'X' and resid 245 through 246 Processing sheet with id=AC4, first strand: chain 'X' and resid 321 through 324 Processing sheet with id=AC5, first strand: chain 'X' and resid 468 through 471 removed outlier: 8.911A pdb=" N ILE X 553 " --> pdb=" O PHE X 419 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS X 421 " --> pdb=" O ILE X 553 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 582 through 583 Processing sheet with id=AC7, first strand: chain 'X' and resid 906 through 909 removed outlier: 8.177A pdb=" N ALA X 902 " --> pdb=" O ASP X1081 " (cutoff:3.500A) removed outlier: 9.728A pdb=" N ASP X1081 " --> pdb=" O ALA X 902 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 906 through 909 removed outlier: 8.177A pdb=" N ALA X 902 " --> pdb=" O ASP X1081 " (cutoff:3.500A) removed outlier: 9.728A pdb=" N ASP X1081 " --> pdb=" O ALA X 902 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU X1080 " --> pdb=" O LYS X 967 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS X 967 " --> pdb=" O LEU X1080 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN X1082 " --> pdb=" O TRP X 965 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TRP X 965 " --> pdb=" O GLN X1082 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER X1038 " --> pdb=" O GLU X1049 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU X1049 " --> pdb=" O SER X1038 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL X1040 " --> pdb=" O ILE X1047 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 917 through 919 removed outlier: 6.878A pdb=" N ILE X 994 " --> pdb=" O LEU X 983 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU X 985 " --> pdb=" O TRP X 992 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TRP X 992 " --> pdb=" O GLU X 985 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 1121 through 1123 Processing sheet with id=AD2, first strand: chain 'X' and resid 1121 through 1123 removed outlier: 3.625A pdb=" N ILE X1201 " --> pdb=" O THR X1224 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 1134 through 1139 Processing sheet with id=AD4, first strand: chain 'X' and resid 1154 through 1156 Processing sheet with id=AD5, first strand: chain 'X' and resid 1228 through 1230 Processing sheet with id=AD6, first strand: chain 'X' and resid 1256 through 1260 779 hydrogen bonds defined for protein. 2118 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: 8.11 Time building geometry restraints manager: 8.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3439 1.32 - 1.45: 5408 1.45 - 1.57: 11354 1.57 - 1.70: 0 1.70 - 1.83: 59 Bond restraints: 20260 Sorted by residual: bond pdb=" N CYS N 88 " pdb=" CA CYS N 88 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.20e-02 6.94e+03 1.26e+01 bond pdb=" C LEU X 624 " pdb=" O LEU X 624 " ideal model delta sigma weight residual 1.237 1.198 0.038 1.17e-02 7.31e+03 1.07e+01 bond pdb=" C PHE X 806 " pdb=" O PHE X 806 " ideal model delta sigma weight residual 1.236 1.194 0.043 1.32e-02 5.74e+03 1.05e+01 bond pdb=" N ILE N 87 " pdb=" CA ILE N 87 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.20e-02 6.94e+03 9.55e+00 bond pdb=" C PRO X 599 " pdb=" O PRO X 599 " ideal model delta sigma weight residual 1.239 1.201 0.038 1.27e-02 6.20e+03 8.86e+00 ... (remaining 20255 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.00: 318 106.00 - 113.01: 10794 113.01 - 120.01: 7090 120.01 - 127.01: 9109 127.01 - 134.02: 160 Bond angle restraints: 27471 Sorted by residual: angle pdb=" N PRO X 424 " pdb=" CA PRO X 424 " pdb=" C PRO X 424 " ideal model delta sigma weight residual 111.38 123.51 -12.13 1.59e+00 3.96e-01 5.82e+01 angle pdb=" N ILE X 869 " pdb=" CA ILE X 869 " pdb=" CB ILE X 869 " ideal model delta sigma weight residual 110.72 118.28 -7.56 1.09e+00 8.42e-01 4.81e+01 angle pdb=" N ASN X 602 " pdb=" CA ASN X 602 " pdb=" C ASN X 602 " ideal model delta sigma weight residual 114.62 108.39 6.23 1.14e+00 7.69e-01 2.99e+01 angle pdb=" CA PHE X 600 " pdb=" CB PHE X 600 " pdb=" CG PHE X 600 " ideal model delta sigma weight residual 113.80 108.43 5.37 1.00e+00 1.00e+00 2.89e+01 angle pdb=" C CYS X 423 " pdb=" N PRO X 424 " pdb=" CA PRO X 424 " ideal model delta sigma weight residual 119.85 125.11 -5.26 1.01e+00 9.80e-01 2.71e+01 ... (remaining 27466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10950 17.97 - 35.93: 1042 35.93 - 53.90: 148 53.90 - 71.86: 41 71.86 - 89.83: 18 Dihedral angle restraints: 12199 sinusoidal: 4997 harmonic: 7202 Sorted by residual: dihedral pdb=" CA LYS N 223 " pdb=" C LYS N 223 " pdb=" N LEU N 224 " pdb=" CA LEU N 224 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA TYR X 139 " pdb=" C TYR X 139 " pdb=" N GLN X 140 " pdb=" CA GLN X 140 " ideal model delta harmonic sigma weight residual -180.00 -158.13 -21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA MET X 22 " pdb=" C MET X 22 " pdb=" N ARG X 23 " pdb=" CA ARG X 23 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 12196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2666 0.071 - 0.143: 361 0.143 - 0.214: 15 0.214 - 0.286: 4 0.286 - 0.357: 3 Chirality restraints: 3049 Sorted by residual: chirality pdb=" CA PRO X 424 " pdb=" N PRO X 424 " pdb=" C PRO X 424 " pdb=" CB PRO X 424 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ASP X1306 " pdb=" N ASP X1306 " pdb=" C ASP X1306 " pdb=" CB ASP X1306 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASP X1304 " pdb=" N ASP X1304 " pdb=" C ASP X1304 " pdb=" CB ASP X1304 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 3046 not shown) Planarity restraints: 3547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP X1304 " 0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C ASP X1304 " -0.074 2.00e-02 2.50e+03 pdb=" O ASP X1304 " 0.029 2.00e-02 2.50e+03 pdb=" N GLU X1305 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR X 771 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C TYR X 771 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR X 771 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS X 772 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA N 429 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ALA N 429 " 0.055 2.00e-02 2.50e+03 pdb=" O ALA N 429 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU N 430 " -0.018 2.00e-02 2.50e+03 ... (remaining 3544 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1498 2.74 - 3.28: 20486 3.28 - 3.82: 32288 3.82 - 4.36: 41007 4.36 - 4.90: 70400 Nonbonded interactions: 165679 Sorted by model distance: nonbonded pdb=" OD1 ASP X1007 " pdb=" N HIS X1008 " model vdw 2.198 2.520 nonbonded pdb=" O ASP N 606 " pdb=" ND2 ASN N 750 " model vdw 2.210 2.520 nonbonded pdb=" OH TYR X 246 " pdb=" O ALA X 732 " model vdw 2.216 2.440 nonbonded pdb=" OH TYR N 51 " pdb=" OE1 GLU N 176 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR N 512 " pdb=" O LYS N 572 " model vdw 2.230 2.440 ... (remaining 165674 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: 1.630 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: 0.020 Extract box with map and model: 7.740 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 50.140 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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 : 0.004 0.057 20260 Z= 0.237 Angle : 0.636 12.132 27471 Z= 0.381 Chirality : 0.048 0.357 3049 Planarity : 0.004 0.063 3547 Dihedral : 14.534 89.826 7542 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 0.40 % 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: -1.08 (0.17), residues: 2413 helix: 0.46 (0.20), residues: 699 sheet: -1.19 (0.27), residues: 359 loop : -1.22 (0.17), residues: 1355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 278 time to evaluate : 2.406 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 285 average time/residue: 0.3106 time to fit residues: 139.1664 Evaluate side-chains 226 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 222 time to evaluate : 2.418 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2047 time to fit residues: 4.9089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 123 optimal weight: 0.1980 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 218 optimal weight: 6.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 ASN N 369 ASN N 426 GLN ** N 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 309 ASN ** X 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1207 ASN ** X1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1233 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 20260 Z= 0.340 Angle : 0.604 8.454 27471 Z= 0.324 Chirality : 0.048 0.185 3049 Planarity : 0.004 0.061 3547 Dihedral : 5.121 26.096 2610 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 1.69 % 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: -0.98 (0.17), residues: 2413 helix: 0.72 (0.19), residues: 722 sheet: -1.23 (0.28), residues: 343 loop : -1.27 (0.16), residues: 1348 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 252 time to evaluate : 2.274 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 27 residues processed: 269 average time/residue: 0.3175 time to fit residues: 135.7010 Evaluate side-chains 256 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 2.503 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2001 time to fit residues: 13.2388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 689 ASN N 942 HIS ** N1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 20260 Z= 0.207 Angle : 0.529 8.543 27471 Z= 0.285 Chirality : 0.045 0.177 3049 Planarity : 0.004 0.066 3547 Dihedral : 4.918 24.643 2610 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 1.02 % 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: -0.77 (0.17), residues: 2413 helix: 1.08 (0.19), residues: 716 sheet: -1.19 (0.27), residues: 367 loop : -1.21 (0.17), residues: 1330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 246 time to evaluate : 2.374 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 263 average time/residue: 0.3103 time to fit residues: 129.0122 Evaluate side-chains 239 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 227 time to evaluate : 2.556 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1949 time to fit residues: 7.7033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 0.2980 chunk 147 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 chunk 232 optimal weight: 0.0570 chunk 114 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 446 GLN ** N1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 396 ASN ** X 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 20260 Z= 0.149 Angle : 0.504 8.963 27471 Z= 0.270 Chirality : 0.044 0.171 3049 Planarity : 0.004 0.066 3547 Dihedral : 4.723 23.870 2610 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 1.51 % 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: -0.58 (0.17), residues: 2413 helix: 1.33 (0.20), residues: 714 sheet: -1.08 (0.28), residues: 351 loop : -1.15 (0.17), residues: 1348 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 251 time to evaluate : 2.439 Fit side-chains outliers start: 34 outliers final: 15 residues processed: 269 average time/residue: 0.3132 time to fit residues: 133.8245 Evaluate side-chains 247 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 232 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1898 time to fit residues: 8.4255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 198 optimal weight: 0.1980 chunk 161 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 209 optimal weight: 0.2980 chunk 58 optimal weight: 0.0870 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 259 GLN ** X 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 721 GLN X1207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 20260 Z= 0.125 Angle : 0.488 8.719 27471 Z= 0.263 Chirality : 0.044 0.174 3049 Planarity : 0.004 0.068 3547 Dihedral : 4.473 23.153 2610 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 1.07 % 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: -0.42 (0.17), residues: 2413 helix: 1.57 (0.20), residues: 713 sheet: -1.04 (0.27), residues: 370 loop : -1.11 (0.17), residues: 1330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 256 time to evaluate : 2.643 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 270 average time/residue: 0.3295 time to fit residues: 141.7437 Evaluate side-chains 243 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 233 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2517 time to fit residues: 7.6210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 9.9990 chunk 209 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 193 optimal weight: 0.1980 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 406 ASN N 737 ASN N1137 ASN ** X 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1207 ASN X1233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 20260 Z= 0.325 Angle : 0.579 8.586 27471 Z= 0.311 Chirality : 0.048 0.174 3049 Planarity : 0.004 0.070 3547 Dihedral : 4.917 24.031 2610 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 1.65 % 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: -0.61 (0.17), residues: 2413 helix: 1.19 (0.19), residues: 737 sheet: -0.94 (0.28), residues: 370 loop : -1.20 (0.17), residues: 1306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 231 time to evaluate : 2.524 Fit side-chains outliers start: 37 outliers final: 23 residues processed: 250 average time/residue: 0.3203 time to fit residues: 127.3813 Evaluate side-chains 245 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 222 time to evaluate : 2.590 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2048 time to fit residues: 12.7631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 232 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 290 ASN N 426 GLN N 547 ASN N 816 ASN ** N1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 887 GLN X1233 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 20260 Z= 0.165 Angle : 0.511 8.828 27471 Z= 0.275 Chirality : 0.044 0.188 3049 Planarity : 0.004 0.067 3547 Dihedral : 4.690 24.137 2610 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.76 % 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: -0.51 (0.17), residues: 2413 helix: 1.49 (0.20), residues: 720 sheet: -1.10 (0.27), residues: 388 loop : -1.16 (0.17), residues: 1305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 233 time to evaluate : 2.518 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 242 average time/residue: 0.3173 time to fit residues: 121.8526 Evaluate side-chains 231 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 222 time to evaluate : 2.386 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2594 time to fit residues: 7.2246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 1.9990 chunk 92 optimal weight: 0.0070 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 426 GLN ** N1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1008 HIS X1233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 20260 Z= 0.179 Angle : 0.511 8.203 27471 Z= 0.274 Chirality : 0.045 0.197 3049 Planarity : 0.004 0.067 3547 Dihedral : 4.614 23.730 2610 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 0.93 % 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: -0.42 (0.17), residues: 2413 helix: 1.59 (0.20), residues: 715 sheet: -1.03 (0.28), residues: 368 loop : -1.12 (0.17), residues: 1330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 2.328 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 242 average time/residue: 0.3100 time to fit residues: 119.5102 Evaluate side-chains 238 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 225 time to evaluate : 2.399 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1843 time to fit residues: 7.9095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 1.9990 chunk 203 optimal weight: 0.2980 chunk 216 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 195 optimal weight: 6.9990 chunk 204 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 142 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 426 GLN ** N1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 662 ASN X1233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 20260 Z= 0.140 Angle : 0.493 10.150 27471 Z= 0.265 Chirality : 0.044 0.174 3049 Planarity : 0.004 0.068 3547 Dihedral : 4.465 22.734 2610 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.27 % 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: -0.34 (0.17), residues: 2413 helix: 1.72 (0.20), residues: 713 sheet: -1.04 (0.28), residues: 368 loop : -1.08 (0.17), residues: 1332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 234 time to evaluate : 2.628 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 236 average time/residue: 0.3268 time to fit residues: 122.0212 Evaluate side-chains 227 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 224 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4013 time to fit residues: 5.1647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 426 GLN ** X 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 662 ASN X 721 GLN X 887 GLN X 890 ASN X1119 ASN X1233 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 20260 Z= 0.311 Angle : 0.572 12.269 27471 Z= 0.306 Chirality : 0.047 0.201 3049 Planarity : 0.004 0.071 3547 Dihedral : 4.814 23.668 2610 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 0.53 % 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: -0.49 (0.17), residues: 2413 helix: 1.38 (0.19), residues: 721 sheet: -0.86 (0.28), residues: 370 loop : -1.16 (0.17), residues: 1322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 227 time to evaluate : 2.442 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 231 average time/residue: 0.3238 time to fit residues: 118.6961 Evaluate side-chains 232 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 224 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1926 time to fit residues: 6.3471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.0370 chunk 58 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 426 GLN ** N1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 890 ASN X1233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122461 restraints weight = 25021.453| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.03 r_work: 0.3313 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 20260 Z= 0.181 Angle : 0.518 8.192 27471 Z= 0.279 Chirality : 0.045 0.216 3049 Planarity : 0.004 0.071 3547 Dihedral : 4.677 23.685 2610 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 0.04 % 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: -0.45 (0.17), residues: 2413 helix: 1.57 (0.20), residues: 709 sheet: -1.08 (0.27), residues: 377 loop : -1.13 (0.17), residues: 1327 =============================================================================== Job complete usr+sys time: 4082.40 seconds wall clock time: 75 minutes 28.59 seconds (4528.59 seconds total)