Starting phenix.real_space_refine on Sat Jun 21 00:59:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arl_43786/06_2025/9arl_43786.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arl_43786/06_2025/9arl_43786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9arl_43786/06_2025/9arl_43786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arl_43786/06_2025/9arl_43786.map" model { file = "/net/cci-nas-00/data/ceres_data/9arl_43786/06_2025/9arl_43786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arl_43786/06_2025/9arl_43786.cif" } resolution = 4.0 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= 0.008 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 71 5.16 5 C 15413 2.51 5 N 3924 2.21 5 O 4646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24054 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1275, 10336 Classifications: {'peptide': 1275} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1236} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 9349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 9349 Classifications: {'peptide': 1147} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1112} Chain breaks: 3 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4369 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 546} Chain breaks: 3 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 14.44, per 1000 atoms: 0.60 Number of scatterers: 24054 At special positions: 0 Unit cell: (108.744, 124.504, 244.28, 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 71 16.00 O 4646 8.00 N 3924 7.00 C 15413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 551 " - pdb=" SG CYS B 723 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 2.8 seconds 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5684 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 36 sheets defined 36.2% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.631A pdb=" N GLY A 57 " --> pdb=" O PRO A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 101 removed outlier: 3.846A pdb=" N THR A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 199 through 203 removed outlier: 4.003A pdb=" N ASP A 203 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.533A pdb=" N THR A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 275 through 299 Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 334 through 347 Processing helix chain 'A' and resid 350 through 359 Processing helix chain 'A' and resid 398 through 405 removed outlier: 4.125A pdb=" N PHE A 401 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLY A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 404 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.802A pdb=" N PHE A 413 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 549 through 556 Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 602 through 618 Processing helix chain 'A' and resid 636 through 642 removed outlier: 3.562A pdb=" N LEU A 641 " --> pdb=" O ILE A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 687 through 721 Processing helix chain 'A' and resid 721 through 754 removed outlier: 3.703A pdb=" N TYR A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 765 through 800 removed outlier: 3.644A pdb=" N LEU A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 826 removed outlier: 3.707A pdb=" N GLY A 804 " --> pdb=" O MET A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.593A pdb=" N LEU A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 861 through 876 Processing helix chain 'A' and resid 954 through 958 Processing helix chain 'A' and resid 1080 through 1092 Processing helix chain 'A' and resid 1210 through 1214 Processing helix chain 'A' and resid 1265 through 1270 Processing helix chain 'A' and resid 1276 through 1280 removed outlier: 3.572A pdb=" N GLY A1279 " --> pdb=" O ARG A1276 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 71 through 92 removed outlier: 3.789A pdb=" N ASN B 92 " --> pdb=" O ARG B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 184 through 201 removed outlier: 3.625A pdb=" N GLU B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 236 removed outlier: 4.415A pdb=" N GLY B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.550A pdb=" N LEU B 243 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 272 Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 280 through 292 removed outlier: 3.548A pdb=" N LYS B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 3.820A pdb=" N ILE B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.881A pdb=" N TYR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.979A pdb=" N LYS B 360 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 430 Processing helix chain 'B' and resid 435 through 439 removed outlier: 3.522A pdb=" N ASP B 438 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B 439 " --> pdb=" O ASP B 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 435 through 439' Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 487 through 494 Processing helix chain 'B' and resid 504 through 514 Processing helix chain 'B' and resid 522 through 542 Processing helix chain 'B' and resid 557 through 563 removed outlier: 3.604A pdb=" N LEU B 560 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 581 Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.682A pdb=" N ILE B 586 " --> pdb=" O ILE B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 609 removed outlier: 3.604A pdb=" N MET B 606 " --> pdb=" O PRO B 603 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN B 608 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 680 removed outlier: 4.421A pdb=" N SER B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN B 647 " --> pdb=" O GLN B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 729 removed outlier: 3.540A pdb=" N ASN B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 755 Processing helix chain 'B' and resid 759 through 770 Processing helix chain 'B' and resid 781 through 788 Processing helix chain 'B' and resid 791 through 801 Processing helix chain 'B' and resid 860 through 864 Processing helix chain 'B' and resid 993 through 1006 Processing helix chain 'B' and resid 1152 through 1156 Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 313 through 331 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.590A pdb=" N GLN C 354 " --> pdb=" O PRO C 351 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TRP C 355 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 4.006A pdb=" N GLN C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR C 408 " --> pdb=" O MET C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 424 Processing helix chain 'C' and resid 425 through 433 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 541 through 547 Processing helix chain 'C' and resid 547 through 565 removed outlier: 3.509A pdb=" N VAL C 552 " --> pdb=" O GLU C 548 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 553 " --> pdb=" O ASP C 549 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA C 554 " --> pdb=" O MET C 550 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER C 561 " --> pdb=" O GLY C 557 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET C 562 " --> pdb=" O THR C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 585 removed outlier: 4.083A pdb=" N LEU C 581 " --> pdb=" O LYS C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 609 Processing helix chain 'C' and resid 612 through 634 Processing helix chain 'C' and resid 641 through 650 Processing helix chain 'C' and resid 654 through 669 Processing helix chain 'C' and resid 670 through 675 Processing helix chain 'C' and resid 682 through 696 Processing helix chain 'C' and resid 703 through 714 removed outlier: 4.532A pdb=" N PHE C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA C 714 " --> pdb=" O GLN C 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 148 removed outlier: 4.572A pdb=" N TYR A 21 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP A 43 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 removed outlier: 6.113A pdb=" N LEU A 127 " --> pdb=" O VAL A 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 214 removed outlier: 4.656A pdb=" N VAL A 373 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 325 Processing sheet with id=AA5, first strand: chain 'A' and resid 426 through 431 Processing sheet with id=AA6, first strand: chain 'A' and resid 479 through 481 removed outlier: 6.358A pdb=" N GLU A 479 " --> pdb=" O ALA A 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.296A pdb=" N ALA A 567 " --> pdb=" O VAL A 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 887 through 890 removed outlier: 4.152A pdb=" N PHE A1072 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N TYR A 883 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 11.481A pdb=" N LYS A1070 " --> pdb=" O TYR A 883 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 887 through 890 removed outlier: 4.152A pdb=" N PHE A1072 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N TYR A 883 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 11.481A pdb=" N LYS A1070 " --> pdb=" O TYR A 883 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A1072 " --> pdb=" O SER A 944 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER A 944 " --> pdb=" O PHE A1072 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU A1074 " --> pdb=" O SER A 942 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER A 942 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE A1031 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU A1035 " --> pdb=" O ILE A1031 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 897 through 900 removed outlier: 3.555A pdb=" N ILE A1047 " --> pdb=" O SER A 936 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 897 through 900 removed outlier: 7.796A pdb=" N MET A1054 " --> pdb=" O CYS A 967 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N CYS A 967 " --> pdb=" O MET A1054 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS A1056 " --> pdb=" O ILE A 965 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE A 965 " --> pdb=" O LYS A1056 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 976 " --> pdb=" O ILE A 964 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASN A 966 " --> pdb=" O TRP A 974 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TRP A 974 " --> pdb=" O ASN A 966 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1122 through 1125 removed outlier: 4.917A pdb=" N MET A1134 " --> pdb=" O LEU A1261 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA A1259 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N MET A1237 " --> pdb=" O ILE A1250 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A1178 " --> pdb=" O MET A1223 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE A1182 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1203 through 1205 removed outlier: 5.420A pdb=" N MET A1237 " --> pdb=" O ILE A1250 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A1178 " --> pdb=" O MET A1223 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS A1159 " --> pdb=" O VAL A1185 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1143 through 1145 Processing sheet with id=AB6, first strand: chain 'B' and resid 131 through 132 removed outlier: 4.693A pdb=" N VAL B 124 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLN B 34 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 41 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 36 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TRP B 40 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 110 through 113 removed outlier: 5.411A pdb=" N GLU B 111 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG B 118 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 181 through 182 removed outlier: 4.105A pdb=" N LEU B 354 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 210 through 215 removed outlier: 6.737A pdb=" N SER B 225 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 391 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 379 through 385 Processing sheet with id=AC2, first strand: chain 'B' and resid 483 through 485 removed outlier: 5.654A pdb=" N ASN B 483 " --> pdb=" O VAL B 500 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 545 through 549 Processing sheet with id=AC4, first strand: chain 'B' and resid 816 through 821 removed outlier: 4.768A pdb=" N LEU B 985 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N ALA B 810 " --> pdb=" O GLU B 983 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N GLU B 983 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 16.289A pdb=" N GLN B 812 " --> pdb=" O TYR B 981 " (cutoff:3.500A) removed outlier: 18.873A pdb=" N TYR B 981 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY B 984 " --> pdb=" O ASP B 844 " (cutoff:3.500A) removed outlier: 10.199A pdb=" N ASP B 844 " --> pdb=" O GLY B 984 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 836 " --> pdb=" O TYR B 847 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 816 through 821 removed outlier: 4.768A pdb=" N LEU B 985 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N ALA B 810 " --> pdb=" O GLU B 983 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N GLU B 983 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 16.289A pdb=" N GLN B 812 " --> pdb=" O TYR B 981 " (cutoff:3.500A) removed outlier: 18.873A pdb=" N TYR B 981 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 985 " --> pdb=" O TYR B 873 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR B 873 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE B 987 " --> pdb=" O SER B 871 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER B 871 " --> pdb=" O ILE B 987 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 949 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU B 953 " --> pdb=" O ILE B 949 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 828 through 831 removed outlier: 8.116A pdb=" N ILE B 970 " --> pdb=" O LYS B 892 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS B 892 " --> pdb=" O ILE B 970 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 900 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY B 890 " --> pdb=" O TRP B 898 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP B 898 " --> pdb=" O GLY B 890 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS B 892 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N CYS B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1025 through 1028 Processing sheet with id=AC8, first strand: chain 'B' and resid 1044 through 1048 removed outlier: 4.399A pdb=" N GLN B1058 " --> pdb=" O GLU B1038 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1062 through 1065 removed outlier: 14.949A pdb=" N VAL B1080 " --> pdb=" O ILE B1094 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N ILE B1094 " --> pdb=" O VAL B1080 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE B1082 " --> pdb=" O ILE B1092 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1062 through 1065 removed outlier: 3.601A pdb=" N ASP B1078 " --> pdb=" O ILE B1114 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1134 through 1135 Processing sheet with id=AD3, first strand: chain 'C' and resid 358 through 361 removed outlier: 3.536A pdb=" N GLN C 360 " --> pdb=" O MET C 387 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 358 through 361 removed outlier: 3.536A pdb=" N GLN C 360 " --> pdb=" O MET C 387 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 740 " --> pdb=" O VAL C 726 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL C 726 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 199 through 206 Processing sheet with id=AD6, first strand: chain 'C' and resid 199 through 206 removed outlier: 6.577A pdb=" N PHE C 256 " --> pdb=" O TYR C 303 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR C 303 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 258 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 263 through 267 Processing sheet with id=AD8, first strand: chain 'C' and resid 441 through 442 removed outlier: 4.002A pdb=" N VAL C 442 " --> pdb=" O THR C 451 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR C 451 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 493 " --> pdb=" O PHE C 506 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE C 506 " --> pdb=" O ASP C 493 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR C 495 " --> pdb=" O GLY C 504 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLY C 504 " --> pdb=" O THR C 495 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 456 through 462 removed outlier: 6.732A pdb=" N SER C 471 " --> pdb=" O PHE C 458 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS C 460 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL C 469 " --> pdb=" O LYS C 460 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER C 472 " --> pdb=" O THR C 495 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR C 495 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 493 " --> pdb=" O PHE C 506 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE C 506 " --> pdb=" O ASP C 493 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR C 495 " --> pdb=" O GLY C 504 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLY C 504 " --> pdb=" O THR C 495 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3213 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: 12.85 Time building geometry restraints manager: 6.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7753 1.34 - 1.46: 4748 1.46 - 1.58: 11928 1.58 - 1.69: 0 1.69 - 1.81: 119 Bond restraints: 24548 Sorted by residual: bond pdb=" N ARG A1276 " pdb=" CA ARG A1276 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.07e+00 bond pdb=" C SER A1274 " pdb=" O SER A1274 " ideal model delta sigma weight residual 1.243 1.231 0.013 9.50e-03 1.11e+04 1.77e+00 bond pdb=" C LEU A1278 " pdb=" O LEU A1278 " ideal model delta sigma weight residual 1.235 1.220 0.015 1.26e-02 6.30e+03 1.39e+00 bond pdb=" CA ILE B 520 " pdb=" CB ILE B 520 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.05e-02 9.07e+03 1.04e+00 bond pdb=" CB VAL A 709 " pdb=" CG1 VAL A 709 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.88e-01 ... (remaining 24543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 32806 1.57 - 3.14: 392 3.14 - 4.71: 51 4.71 - 6.28: 11 6.28 - 7.84: 4 Bond angle restraints: 33264 Sorted by residual: angle pdb=" CA SER A1274 " pdb=" C SER A1274 " pdb=" N SER A1275 " ideal model delta sigma weight residual 119.98 116.32 3.66 8.50e-01 1.38e+00 1.86e+01 angle pdb=" N ARG A1273 " pdb=" CA ARG A1273 " pdb=" C ARG A1273 " ideal model delta sigma weight residual 109.02 115.88 -6.86 1.68e+00 3.54e-01 1.67e+01 angle pdb=" C ARG A1273 " pdb=" CA ARG A1273 " pdb=" CB ARG A1273 " ideal model delta sigma weight residual 115.89 110.67 5.22 1.32e+00 5.74e-01 1.57e+01 angle pdb=" C SER A1274 " pdb=" CA SER A1274 " pdb=" CB SER A1274 " ideal model delta sigma weight residual 117.23 112.24 4.99 1.36e+00 5.41e-01 1.35e+01 angle pdb=" N ILE A1247 " pdb=" CA ILE A1247 " pdb=" C ILE A1247 " ideal model delta sigma weight residual 113.07 108.91 4.16 1.36e+00 5.41e-01 9.34e+00 ... (remaining 33259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 13786 17.67 - 35.34: 743 35.34 - 53.01: 137 53.01 - 70.68: 28 70.68 - 88.36: 13 Dihedral angle restraints: 14707 sinusoidal: 5884 harmonic: 8823 Sorted by residual: dihedral pdb=" CA ILE A1247 " pdb=" C ILE A1247 " pdb=" N GLY A1248 " pdb=" CA GLY A1248 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE A 627 " pdb=" C ILE A 627 " pdb=" N ALA A 628 " pdb=" CA ALA A 628 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" N ARG A1276 " pdb=" C ARG A1276 " pdb=" CA ARG A1276 " pdb=" CB ARG A1276 " ideal model delta harmonic sigma weight residual 122.80 132.96 -10.16 0 2.50e+00 1.60e-01 1.65e+01 ... (remaining 14704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3343 0.074 - 0.147: 352 0.147 - 0.221: 2 0.221 - 0.295: 1 0.295 - 0.369: 1 Chirality restraints: 3699 Sorted by residual: chirality pdb=" CA ARG A1276 " pdb=" N ARG A1276 " pdb=" C ARG A1276 " pdb=" CB ARG A1276 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA SER A1274 " pdb=" N SER A1274 " pdb=" C SER A1274 " pdb=" CB SER A1274 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA LEU A1278 " pdb=" N LEU A1278 " pdb=" C LEU A1278 " pdb=" CB LEU A1278 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3696 not shown) Planarity restraints: 4286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 967 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C CYS A 967 " 0.037 2.00e-02 2.50e+03 pdb=" O CYS A 967 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 968 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 641 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C TRP B 641 " -0.036 2.00e-02 2.50e+03 pdb=" O TRP B 641 " 0.013 2.00e-02 2.50e+03 pdb=" N THR B 642 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 532 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO C 533 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 533 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 533 " 0.022 5.00e-02 4.00e+02 ... (remaining 4283 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 673 2.70 - 3.25: 24778 3.25 - 3.80: 39456 3.80 - 4.35: 52063 4.35 - 4.90: 86358 Nonbonded interactions: 203328 Sorted by model distance: nonbonded pdb=" N ASP A 275 " pdb=" OD1 ASP A 275 " model vdw 2.147 3.120 nonbonded pdb=" O GLY A 179 " pdb=" OH TYR A 321 " model vdw 2.201 3.040 nonbonded pdb=" O LYS A 838 " pdb=" ND2 ASN A 842 " model vdw 2.205 3.120 nonbonded pdb=" O LEU C 616 " pdb=" ND2 ASN C 620 " model vdw 2.208 3.120 nonbonded pdb=" OH TYR A 980 " pdb=" O ILE A1148 " model vdw 2.209 3.040 ... (remaining 203323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 10.750 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: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.200 Process input model: 59.590 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 : 0.003 0.033 24550 Z= 0.155 Angle : 0.481 7.844 33268 Z= 0.266 Chirality : 0.043 0.369 3699 Planarity : 0.003 0.039 4286 Dihedral : 11.646 88.355 9017 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 3.40 % Allowed : 6.09 % Favored : 90.51 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.33 % 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: 0.50 (0.16), residues: 2961 helix: 1.69 (0.17), residues: 936 sheet: -0.07 (0.23), residues: 530 loop : -0.34 (0.17), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 641 HIS 0.002 0.001 HIS C 398 PHE 0.015 0.001 PHE A 464 TYR 0.017 0.001 TYR B 873 ARG 0.003 0.000 ARG A1023 Details of bonding type rmsd hydrogen bonds : bond 0.13191 ( 1109) hydrogen bonds : angle 5.98130 ( 3213) SS BOND : bond 0.00150 ( 2) SS BOND : angle 1.90659 ( 4) covalent geometry : bond 0.00344 (24548) covalent geometry : angle 0.48032 (33264) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 281 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6774 (mtp) cc_final: 0.6489 (mtt) REVERT: A 315 ASN cc_start: 0.8362 (m110) cc_final: 0.8086 (m110) REVERT: A 373 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7957 (m) REVERT: A 497 ASP cc_start: 0.8299 (t0) cc_final: 0.7960 (t0) REVERT: A 500 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7059 (mp10) REVERT: A 606 TRP cc_start: 0.7942 (t60) cc_final: 0.7688 (t60) REVERT: A 620 GLU cc_start: 0.8290 (tt0) cc_final: 0.8060 (tt0) REVERT: A 732 MET cc_start: 0.7792 (mmm) cc_final: 0.7576 (tpt) REVERT: A 748 ASN cc_start: 0.7420 (t0) cc_final: 0.7172 (t0) REVERT: A 759 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8391 (tmtt) REVERT: A 989 ASP cc_start: 0.6821 (p0) cc_final: 0.6586 (p0) REVERT: A 1134 MET cc_start: 0.8805 (tpt) cc_final: 0.8424 (mmm) REVERT: A 1209 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8187 (tm) REVERT: B 127 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8625 (p0) REVERT: B 176 TYR cc_start: 0.8144 (p90) cc_final: 0.7780 (p90) REVERT: B 355 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8152 (tt) REVERT: B 381 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7313 (tmt) REVERT: B 473 GLN cc_start: 0.7629 (tt0) cc_final: 0.7246 (mt0) REVERT: B 1154 TYR cc_start: 0.8610 (m-80) cc_final: 0.8072 (m-80) outliers start: 91 outliers final: 44 residues processed: 351 average time/residue: 0.3350 time to fit residues: 190.9219 Evaluate side-chains 272 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 881 LYS Chi-restraints excluded: chain B residue 901 TYR Chi-restraints excluded: chain B residue 1118 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1144 TRP Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 269 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 139 GLN A 227 HIS A 311 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN A 912 ASN A1126 ASN A1151 ASN B 320 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN B 692 ASN ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN B 903 GLN B 915 ASN B 944 GLN B1108 ASN C 285 ASN C 484 ASN C 498 GLN ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.123788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.093741 restraints weight = 52791.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092573 restraints weight = 42476.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.092868 restraints weight = 33728.753| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24550 Z= 0.152 Angle : 0.519 11.967 33268 Z= 0.277 Chirality : 0.043 0.164 3699 Planarity : 0.003 0.039 4286 Dihedral : 6.517 57.621 3316 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.88 % Allowed : 8.93 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.59 (0.16), residues: 2961 helix: 1.77 (0.17), residues: 934 sheet: -0.00 (0.23), residues: 523 loop : -0.30 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 641 HIS 0.003 0.001 HIS A 230 PHE 0.016 0.001 PHE A 374 TYR 0.020 0.001 TYR A 251 ARG 0.005 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 1109) hydrogen bonds : angle 5.05827 ( 3213) SS BOND : bond 0.00219 ( 2) SS BOND : angle 1.59631 ( 4) covalent geometry : bond 0.00343 (24548) covalent geometry : angle 0.51857 (33264) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 250 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7335 (mtp) cc_final: 0.7008 (mtt) REVERT: A 118 TRP cc_start: 0.7709 (m-10) cc_final: 0.7203 (m-10) REVERT: A 315 ASN cc_start: 0.8025 (m110) cc_final: 0.7743 (m110) REVERT: A 497 ASP cc_start: 0.7927 (t0) cc_final: 0.7633 (t0) REVERT: A 500 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: A 748 ASN cc_start: 0.7571 (t0) cc_final: 0.7178 (t0) REVERT: B 176 TYR cc_start: 0.7888 (p90) cc_final: 0.7562 (p90) REVERT: B 381 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7771 (tpt) REVERT: B 737 MET cc_start: 0.7337 (mmm) cc_final: 0.6812 (tpp) REVERT: B 833 LYS cc_start: 0.8462 (pptt) cc_final: 0.8116 (pptt) REVERT: B 1003 LYS cc_start: 0.8839 (tptt) cc_final: 0.8478 (tttp) REVERT: B 1154 TYR cc_start: 0.8470 (m-80) cc_final: 0.8240 (m-80) outliers start: 77 outliers final: 51 residues processed: 309 average time/residue: 0.3504 time to fit residues: 175.7174 Evaluate side-chains 275 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 222 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 881 LYS Chi-restraints excluded: chain B residue 901 TYR Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1118 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1144 TRP Chi-restraints excluded: chain C residue 368 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 202 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 412 ASN A 645 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN A1115 ASN B 320 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.121700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091444 restraints weight = 53102.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090080 restraints weight = 43053.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090254 restraints weight = 37699.033| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24550 Z= 0.227 Angle : 0.574 11.320 33268 Z= 0.303 Chirality : 0.045 0.209 3699 Planarity : 0.003 0.040 4286 Dihedral : 6.435 56.276 3299 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.66 % Allowed : 10.54 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.33 (0.16), residues: 2961 helix: 1.47 (0.17), residues: 938 sheet: -0.11 (0.23), residues: 524 loop : -0.40 (0.17), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 641 HIS 0.005 0.001 HIS A 227 PHE 0.017 0.002 PHE A 585 TYR 0.020 0.002 TYR B 873 ARG 0.005 0.000 ARG C 592 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 1109) hydrogen bonds : angle 4.99878 ( 3213) SS BOND : bond 0.00181 ( 2) SS BOND : angle 1.58294 ( 4) covalent geometry : bond 0.00526 (24548) covalent geometry : angle 0.57420 (33264) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 234 time to evaluate : 3.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7379 (mtp) cc_final: 0.7075 (mtt) REVERT: A 315 ASN cc_start: 0.8074 (m110) cc_final: 0.7833 (m110) REVERT: A 497 ASP cc_start: 0.8015 (t0) cc_final: 0.7686 (t0) REVERT: A 500 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: A 606 TRP cc_start: 0.7291 (t60) cc_final: 0.7041 (t60) REVERT: B 176 TYR cc_start: 0.7988 (p90) cc_final: 0.7663 (p90) REVERT: B 1151 MET cc_start: 0.4524 (pmm) cc_final: 0.4040 (pmm) REVERT: B 1154 TYR cc_start: 0.8453 (m-80) cc_final: 0.8239 (m-80) outliers start: 98 outliers final: 65 residues processed: 305 average time/residue: 0.3252 time to fit residues: 164.2009 Evaluate side-chains 283 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 217 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 881 LYS Chi-restraints excluded: chain B residue 901 TYR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1037 TYR Chi-restraints excluded: chain B residue 1118 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1144 TRP Chi-restraints excluded: chain C residue 368 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 173 optimal weight: 1.9990 chunk 271 optimal weight: 40.0000 chunk 256 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 170 optimal weight: 0.0570 chunk 102 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN A 912 ASN A1026 ASN A1038 GLN B 320 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.123428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.093612 restraints weight = 53607.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092561 restraints weight = 40484.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093098 restraints weight = 33798.013| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24550 Z= 0.133 Angle : 0.505 13.002 33268 Z= 0.268 Chirality : 0.043 0.181 3699 Planarity : 0.003 0.038 4286 Dihedral : 6.066 56.194 3287 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.99 % Allowed : 11.81 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.53 (0.16), residues: 2961 helix: 1.72 (0.17), residues: 938 sheet: -0.09 (0.23), residues: 511 loop : -0.31 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 706 HIS 0.003 0.001 HIS A 227 PHE 0.018 0.001 PHE A 464 TYR 0.015 0.001 TYR A 636 ARG 0.006 0.000 ARG C 592 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 1109) hydrogen bonds : angle 4.74605 ( 3213) SS BOND : bond 0.00632 ( 2) SS BOND : angle 2.24619 ( 4) covalent geometry : bond 0.00301 (24548) covalent geometry : angle 0.50424 (33264) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 241 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7366 (mtp) cc_final: 0.7055 (mtt) REVERT: A 15 ASN cc_start: 0.7905 (t0) cc_final: 0.7677 (t0) REVERT: A 315 ASN cc_start: 0.7913 (m110) cc_final: 0.7676 (m110) REVERT: A 352 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: A 497 ASP cc_start: 0.8055 (t0) cc_final: 0.7750 (t0) REVERT: A 500 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7097 (mp10) REVERT: A 732 MET cc_start: 0.7468 (mmm) cc_final: 0.6572 (mmm) REVERT: B 127 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7581 (p0) REVERT: B 176 TYR cc_start: 0.7960 (p90) cc_final: 0.7596 (p90) REVERT: B 1003 LYS cc_start: 0.8845 (tptt) cc_final: 0.8578 (tttp) REVERT: B 1151 MET cc_start: 0.4576 (pmm) cc_final: 0.4037 (pmm) REVERT: B 1154 TYR cc_start: 0.8409 (m-80) cc_final: 0.8169 (m-80) outliers start: 80 outliers final: 60 residues processed: 300 average time/residue: 0.3149 time to fit residues: 157.0136 Evaluate side-chains 283 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 220 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 1026 ASN Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 881 LYS Chi-restraints excluded: chain B residue 901 TYR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1037 TYR Chi-restraints excluded: chain B residue 1118 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1144 TRP Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 556 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 293 optimal weight: 30.0000 chunk 242 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 chunk 66 optimal weight: 0.2980 chunk 248 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 142 optimal weight: 0.5980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 362 ASN A 470 ASN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN B 320 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 ASN B 769 GLN ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.120583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.090696 restraints weight = 54103.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088966 restraints weight = 42359.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089347 restraints weight = 38370.877| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 24550 Z= 0.267 Angle : 0.604 14.420 33268 Z= 0.319 Chirality : 0.045 0.187 3699 Planarity : 0.004 0.039 4286 Dihedral : 6.302 56.110 3283 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 3.85 % Allowed : 12.37 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.17 (0.16), residues: 2961 helix: 1.35 (0.17), residues: 940 sheet: -0.33 (0.23), residues: 513 loop : -0.46 (0.17), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 641 HIS 0.005 0.001 HIS A 227 PHE 0.020 0.002 PHE A 585 TYR 0.022 0.002 TYR B 873 ARG 0.004 0.000 ARG C 592 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 1109) hydrogen bonds : angle 4.92792 ( 3213) SS BOND : bond 0.00703 ( 2) SS BOND : angle 4.69864 ( 4) covalent geometry : bond 0.00620 (24548) covalent geometry : angle 0.60211 (33264) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 219 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7335 (mtp) cc_final: 0.7025 (mtt) REVERT: A 15 ASN cc_start: 0.8034 (t0) cc_final: 0.7782 (t0) REVERT: A 315 ASN cc_start: 0.7995 (m110) cc_final: 0.7759 (m110) REVERT: A 352 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: A 497 ASP cc_start: 0.8030 (t0) cc_final: 0.7725 (t0) REVERT: A 500 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7142 (mp10) REVERT: A 673 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7694 (tp) REVERT: A 732 MET cc_start: 0.7543 (mmm) cc_final: 0.6664 (mmm) REVERT: B 127 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7652 (p0) REVERT: B 176 TYR cc_start: 0.8033 (p90) cc_final: 0.7735 (p90) REVERT: B 724 VAL cc_start: 0.7593 (OUTLIER) cc_final: 0.7352 (p) REVERT: B 1151 MET cc_start: 0.4907 (pmm) cc_final: 0.4339 (pmm) REVERT: B 1154 TYR cc_start: 0.8483 (m-80) cc_final: 0.8156 (m-80) outliers start: 103 outliers final: 79 residues processed: 300 average time/residue: 0.3162 time to fit residues: 158.1373 Evaluate side-chains 293 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 209 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 881 LYS Chi-restraints excluded: chain B residue 901 TYR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1037 TYR Chi-restraints excluded: chain B residue 1118 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1144 TRP Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 556 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 48 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 259 optimal weight: 7.9990 chunk 218 optimal weight: 0.2980 chunk 225 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 196 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 283 optimal weight: 40.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 470 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN B 320 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 GLN ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.123358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093738 restraints weight = 52915.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092555 restraints weight = 39960.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092601 restraints weight = 33758.811| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24550 Z= 0.120 Angle : 0.507 11.728 33268 Z= 0.268 Chirality : 0.043 0.203 3699 Planarity : 0.003 0.037 4286 Dihedral : 5.992 56.003 3281 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.03 % Allowed : 13.68 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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 (0.16), residues: 2961 helix: 1.70 (0.17), residues: 944 sheet: -0.13 (0.23), residues: 515 loop : -0.35 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 706 HIS 0.002 0.000 HIS A 223 PHE 0.018 0.001 PHE A 464 TYR 0.015 0.001 TYR A 636 ARG 0.006 0.000 ARG C 184 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 1109) hydrogen bonds : angle 4.66183 ( 3213) SS BOND : bond 0.00276 ( 2) SS BOND : angle 0.91859 ( 4) covalent geometry : bond 0.00269 (24548) covalent geometry : angle 0.50671 (33264) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 225 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7288 (mtp) cc_final: 0.6978 (mtt) REVERT: A 15 ASN cc_start: 0.7916 (t0) cc_final: 0.7685 (t0) REVERT: A 34 LYS cc_start: 0.8022 (tttt) cc_final: 0.7686 (tttm) REVERT: A 315 ASN cc_start: 0.7926 (m110) cc_final: 0.7680 (m110) REVERT: A 352 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7032 (m-30) REVERT: A 428 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7034 (tp) REVERT: A 732 MET cc_start: 0.7477 (mmm) cc_final: 0.6531 (mmm) REVERT: B 127 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7739 (p0) REVERT: B 176 TYR cc_start: 0.7983 (p90) cc_final: 0.7625 (p90) REVERT: B 550 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6954 (pt) REVERT: B 1003 LYS cc_start: 0.8875 (tptt) cc_final: 0.8639 (tttp) REVERT: B 1151 MET cc_start: 0.4769 (pmm) cc_final: 0.4172 (pmm) REVERT: B 1154 TYR cc_start: 0.8496 (m-80) cc_final: 0.8275 (m-80) outliers start: 81 outliers final: 64 residues processed: 292 average time/residue: 0.3263 time to fit residues: 158.1088 Evaluate side-chains 284 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 216 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 881 LYS Chi-restraints excluded: chain B residue 901 TYR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1037 TYR Chi-restraints excluded: chain B residue 1118 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1144 TRP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 381 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 266 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.122551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093004 restraints weight = 53579.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091606 restraints weight = 41787.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.091989 restraints weight = 38150.282| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24550 Z= 0.162 Angle : 0.535 14.430 33268 Z= 0.280 Chirality : 0.043 0.189 3699 Planarity : 0.003 0.037 4286 Dihedral : 5.957 56.098 3279 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.14 % Allowed : 14.16 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.47 (0.16), residues: 2961 helix: 1.71 (0.17), residues: 939 sheet: -0.20 (0.23), residues: 525 loop : -0.35 (0.17), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.003 0.001 HIS A 227 PHE 0.022 0.001 PHE A 374 TYR 0.017 0.001 TYR A 251 ARG 0.004 0.000 ARG C 592 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 1109) hydrogen bonds : angle 4.68453 ( 3213) SS BOND : bond 0.00131 ( 2) SS BOND : angle 1.17930 ( 4) covalent geometry : bond 0.00375 (24548) covalent geometry : angle 0.53485 (33264) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 223 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7324 (mtp) cc_final: 0.6916 (mtt) REVERT: A 34 LYS cc_start: 0.8030 (tttt) cc_final: 0.7704 (tttm) REVERT: A 315 ASN cc_start: 0.7891 (m110) cc_final: 0.7671 (m110) REVERT: A 352 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7063 (m-30) REVERT: A 428 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7051 (tp) REVERT: A 500 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7142 (mp10) REVERT: A 732 MET cc_start: 0.7529 (mmm) cc_final: 0.6388 (mmm) REVERT: B 127 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7707 (p0) REVERT: B 176 TYR cc_start: 0.8002 (p90) cc_final: 0.7674 (p90) REVERT: B 724 VAL cc_start: 0.7524 (OUTLIER) cc_final: 0.7297 (p) REVERT: B 1003 LYS cc_start: 0.8870 (tptt) cc_final: 0.8641 (tttp) REVERT: B 1029 TYR cc_start: 0.8505 (t80) cc_final: 0.8005 (t80) REVERT: B 1111 LYS cc_start: 0.7912 (mppt) cc_final: 0.7394 (mmtp) REVERT: B 1151 MET cc_start: 0.4622 (pmm) cc_final: 0.4040 (pmm) REVERT: B 1154 TYR cc_start: 0.8444 (m-80) cc_final: 0.8190 (m-80) outliers start: 84 outliers final: 70 residues processed: 291 average time/residue: 0.3165 time to fit residues: 152.7974 Evaluate side-chains 291 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 216 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 881 LYS Chi-restraints excluded: chain B residue 901 TYR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1037 TYR Chi-restraints excluded: chain B residue 1118 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1144 TRP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 556 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 129 optimal weight: 0.7980 chunk 226 optimal weight: 0.9990 chunk 291 optimal weight: 20.0000 chunk 207 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 249 optimal weight: 20.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 470 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.122029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092290 restraints weight = 53534.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.091063 restraints weight = 40421.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091696 restraints weight = 33732.489| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24550 Z= 0.181 Angle : 0.548 13.938 33268 Z= 0.287 Chirality : 0.044 0.189 3699 Planarity : 0.003 0.037 4286 Dihedral : 6.017 56.142 3279 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.36 % Allowed : 14.16 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.40 (0.16), residues: 2961 helix: 1.67 (0.17), residues: 938 sheet: -0.25 (0.22), residues: 538 loop : -0.39 (0.17), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.003 0.001 HIS A 227 PHE 0.018 0.001 PHE B1031 TYR 0.017 0.001 TYR B 873 ARG 0.002 0.000 ARG A 48 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 1109) hydrogen bonds : angle 4.71600 ( 3213) SS BOND : bond 0.00155 ( 2) SS BOND : angle 1.20387 ( 4) covalent geometry : bond 0.00418 (24548) covalent geometry : angle 0.54798 (33264) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 222 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7271 (mtp) cc_final: 0.6867 (mtt) REVERT: A 34 LYS cc_start: 0.8043 (tttt) cc_final: 0.7673 (tttm) REVERT: A 315 ASN cc_start: 0.7928 (m110) cc_final: 0.7727 (m110) REVERT: A 352 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: A 428 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7121 (tp) REVERT: A 500 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7057 (mp10) REVERT: A 673 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7613 (tp) REVERT: B 127 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7744 (p0) REVERT: B 176 TYR cc_start: 0.7990 (p90) cc_final: 0.7623 (p90) REVERT: B 724 VAL cc_start: 0.7456 (OUTLIER) cc_final: 0.7221 (p) REVERT: B 923 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6276 (mt) REVERT: B 1003 LYS cc_start: 0.8909 (tptt) cc_final: 0.8694 (tttp) REVERT: B 1111 LYS cc_start: 0.7906 (mppt) cc_final: 0.7404 (mmtp) REVERT: B 1151 MET cc_start: 0.4747 (pmm) cc_final: 0.4118 (pmm) REVERT: B 1154 TYR cc_start: 0.8452 (m-80) cc_final: 0.8160 (m-80) outliers start: 90 outliers final: 74 residues processed: 297 average time/residue: 0.3187 time to fit residues: 157.6759 Evaluate side-chains 298 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 217 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 881 LYS Chi-restraints excluded: chain B residue 901 TYR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1037 TYR Chi-restraints excluded: chain B residue 1118 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1144 TRP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 381 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 161 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 272 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 412 ASN A 470 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN B 406 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.122267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.092739 restraints weight = 53613.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091491 restraints weight = 41692.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092103 restraints weight = 33701.779| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24550 Z= 0.165 Angle : 0.545 13.463 33268 Z= 0.285 Chirality : 0.043 0.191 3699 Planarity : 0.003 0.037 4286 Dihedral : 6.005 56.150 3277 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.33 % Allowed : 14.13 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.43 (0.16), residues: 2961 helix: 1.70 (0.17), residues: 938 sheet: -0.24 (0.22), residues: 538 loop : -0.38 (0.17), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.003 0.001 HIS A 227 PHE 0.018 0.001 PHE B1031 TYR 0.017 0.001 TYR A 251 ARG 0.002 0.000 ARG A 48 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 1109) hydrogen bonds : angle 4.68922 ( 3213) SS BOND : bond 0.00145 ( 2) SS BOND : angle 1.19690 ( 4) covalent geometry : bond 0.00382 (24548) covalent geometry : angle 0.54440 (33264) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 220 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7296 (mtp) cc_final: 0.6883 (mtt) REVERT: A 34 LYS cc_start: 0.8029 (tttt) cc_final: 0.7666 (tttm) REVERT: A 352 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7062 (m-30) REVERT: A 428 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7054 (tp) REVERT: A 500 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7069 (mp10) REVERT: A 673 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7614 (tp) REVERT: B 127 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7723 (p0) REVERT: B 176 TYR cc_start: 0.7971 (p90) cc_final: 0.7638 (p90) REVERT: B 724 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7220 (p) REVERT: B 923 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6172 (mt) REVERT: B 1003 LYS cc_start: 0.8895 (tptt) cc_final: 0.8680 (tttp) REVERT: B 1151 MET cc_start: 0.4682 (pmm) cc_final: 0.4070 (pmm) REVERT: B 1154 TYR cc_start: 0.8418 (m-80) cc_final: 0.8179 (m-80) outliers start: 89 outliers final: 74 residues processed: 292 average time/residue: 0.3199 time to fit residues: 155.8601 Evaluate side-chains 292 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 211 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 881 LYS Chi-restraints excluded: chain B residue 901 TYR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1037 TYR Chi-restraints excluded: chain B residue 1118 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1144 TRP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 381 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 83 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 287 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 213 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 166 optimal weight: 0.2980 chunk 106 optimal weight: 0.8980 chunk 226 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 470 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN B 406 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.123427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093658 restraints weight = 53356.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092474 restraints weight = 39779.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093155 restraints weight = 34068.075| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24550 Z= 0.121 Angle : 0.523 15.164 33268 Z= 0.274 Chirality : 0.043 0.193 3699 Planarity : 0.003 0.038 4286 Dihedral : 5.910 56.341 3277 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.99 % Allowed : 14.50 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2961 helix: 1.82 (0.17), residues: 943 sheet: -0.15 (0.23), residues: 523 loop : -0.36 (0.17), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 706 HIS 0.002 0.000 HIS A 223 PHE 0.024 0.001 PHE A 464 TYR 0.018 0.001 TYR A 502 ARG 0.002 0.000 ARG A 48 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 1109) hydrogen bonds : angle 4.59223 ( 3213) SS BOND : bond 0.00125 ( 2) SS BOND : angle 1.18174 ( 4) covalent geometry : bond 0.00275 (24548) covalent geometry : angle 0.52281 (33264) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 221 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7283 (mtp) cc_final: 0.6867 (mtt) REVERT: A 34 LYS cc_start: 0.8004 (tttt) cc_final: 0.7592 (tttm) REVERT: A 352 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6972 (m-30) REVERT: A 428 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7096 (tp) REVERT: A 500 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: A 673 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7583 (tp) REVERT: B 127 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7688 (p0) REVERT: B 176 TYR cc_start: 0.7951 (p90) cc_final: 0.7607 (p90) REVERT: B 724 VAL cc_start: 0.7437 (OUTLIER) cc_final: 0.7211 (p) REVERT: B 901 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.6443 (m-80) REVERT: B 923 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6300 (mt) REVERT: B 1003 LYS cc_start: 0.8880 (tptt) cc_final: 0.8673 (tttp) REVERT: B 1151 MET cc_start: 0.4630 (pmm) cc_final: 0.4031 (pmm) REVERT: B 1154 TYR cc_start: 0.8431 (m-80) cc_final: 0.8203 (m-80) outliers start: 80 outliers final: 66 residues processed: 286 average time/residue: 0.3179 time to fit residues: 151.6887 Evaluate side-chains 291 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 217 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 881 LYS Chi-restraints excluded: chain B residue 901 TYR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 1037 TYR Chi-restraints excluded: chain B residue 1118 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1144 TRP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 381 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 182 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 chunk 85 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 470 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 ASN B 406 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.122356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.093873 restraints weight = 53603.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093589 restraints weight = 50308.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.094533 restraints weight = 39974.664| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24550 Z= 0.171 Angle : 0.552 15.236 33268 Z= 0.287 Chirality : 0.044 0.190 3699 Planarity : 0.003 0.038 4286 Dihedral : 5.868 56.467 3275 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.03 % Allowed : 14.46 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.46 (0.16), residues: 2961 helix: 1.72 (0.17), residues: 945 sheet: -0.23 (0.22), residues: 538 loop : -0.35 (0.17), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.003 0.001 HIS A 227 PHE 0.024 0.001 PHE A 464 TYR 0.019 0.001 TYR B 901 ARG 0.003 0.000 ARG A1192 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 1109) hydrogen bonds : angle 4.64928 ( 3213) SS BOND : bond 0.00133 ( 2) SS BOND : angle 1.13539 ( 4) covalent geometry : bond 0.00396 (24548) covalent geometry : angle 0.55170 (33264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7294.86 seconds wall clock time: 128 minutes 20.19 seconds (7700.19 seconds total)