Starting phenix.real_space_refine on Fri Sep 19 07:47:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arl_43786/09_2025/9arl_43786.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arl_43786/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9arl_43786/09_2025/9arl_43786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arl_43786/09_2025/9arl_43786.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9arl_43786/09_2025/9arl_43786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arl_43786/09_2025/9arl_43786.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1} 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: {'ASP:plan': 4, 'GLU:plan': 3, 'ASN:plan1': 3, 'ARG:plan': 1} 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: 4.89, per 1000 atoms: 0.20 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: 1.77 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.99 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: 5.94 Time building geometry restraints manager: 2.46 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: 12.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.350 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.660 ------------------------------------------------------------------------------- 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 : 10.92 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A1023 TYR 0.017 0.001 TYR B 873 PHE 0.015 0.001 PHE A 464 TRP 0.009 0.001 TRP B 641 HIS 0.002 0.001 HIS C 398 Details of bonding type rmsd covalent geometry : bond 0.00344 (24548) covalent geometry : angle 0.48032 (33264) SS BOND : bond 0.00150 ( 2) SS BOND : angle 1.90659 ( 4) hydrogen bonds : bond 0.13191 ( 1109) hydrogen bonds : angle 5.98130 ( 3213) *********************** 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 : 0.776 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: 0.6774 (mtp) cc_final: 0.6486 (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: 0.7958 (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: 0.7687 (t60) REVERT: A 620 GLU cc_start: 0.8290 (tt0) cc_final: 0.8067 (tt0) REVERT: A 759 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8392 (tmtt) REVERT: A 989 ASP cc_start: 0.6821 (p0) cc_final: 0.6585 (p0) REVERT: A 1134 MET cc_start: 0.8805 (tpt) cc_final: 0.8423 (mmm) REVERT: A 1209 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8189 (tm) REVERT: A 1239 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8170 (tp) 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: 0.7781 (p90) REVERT: B 355 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8153 (tt) REVERT: B 381 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7312 (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: 43 residues processed: 351 average time/residue: 0.1502 time to fit residues: 85.3259 Evaluate side-chains 271 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0870 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- 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 311 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN A 912 ASN A1021 ASN A1126 ASN A1151 ASN B 320 ASN B 604 ASN B 643 GLN B 692 ASN B 726 GLN 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.125351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095292 restraints weight = 52459.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.094220 restraints weight = 39276.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094323 restraints weight = 32822.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.094832 restraints weight = 32397.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.094977 restraints weight = 26999.624| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 24550 Z= 0.116 Angle : 0.504 12.075 33268 Z= 0.269 Chirality : 0.043 0.170 3699 Planarity : 0.003 0.039 4286 Dihedral : 6.416 57.250 3316 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.58 % Allowed : 9.01 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.16), residues: 2961 helix: 1.88 (0.17), residues: 934 sheet: 0.03 (0.23), residues: 521 loop : -0.23 (0.17), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 592 TYR 0.021 0.001 TYR A 251 PHE 0.018 0.001 PHE A 419 TRP 0.010 0.001 TRP A1266 HIS 0.003 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00249 (24548) covalent geometry : angle 0.50399 (33264) SS BOND : bond 0.00265 ( 2) SS BOND : angle 1.49108 ( 4) hydrogen bonds : bond 0.04065 ( 1109) hydrogen bonds : angle 4.95740 ( 3213) *********************** 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 333 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 264 time to evaluate : 0.780 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: 0.7290 (mtp) cc_final: 0.6955 (mtt) REVERT: A 315 ASN cc_start: 0.8016 (m110) cc_final: 0.7774 (m110) REVERT: A 345 LEU cc_start: 0.8354 (mm) cc_final: 0.8149 (mt) REVERT: A 428 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7072 (tt) REVERT: A 497 ASP cc_start: 0.7938 (t0) cc_final: 0.7644 (t0) REVERT: A 500 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: B 176 TYR cc_start: 0.7851 (p90) cc_final: 0.7520 (p90) REVERT: B 541 MET cc_start: 0.7659 (tpp) cc_final: 0.7315 (mpp) REVERT: B 833 LYS cc_start: 0.8442 (pptt) cc_final: 0.8138 (pptt) REVERT: B 1003 LYS cc_start: 0.8840 (tptt) cc_final: 0.8562 (tttp) REVERT: B 1154 TYR cc_start: 0.8503 (m-80) cc_final: 0.8230 (m-80) outliers start: 69 outliers final: 45 residues processed: 315 average time/residue: 0.1473 time to fit residues: 75.6456 Evaluate side-chains 274 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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 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 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 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 533 ILE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 637 LEU 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 256 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 204 optimal weight: 1.9990 chunk 277 optimal weight: 30.0000 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 147 optimal weight: 0.5980 chunk 266 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 645 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** B 396 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 = 0.3949 r_free = 0.3949 target = 0.124994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.094711 restraints weight = 52647.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094086 restraints weight = 37641.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093930 restraints weight = 32232.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094658 restraints weight = 31406.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.094712 restraints weight = 26869.160| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24550 Z= 0.123 Angle : 0.498 10.219 33268 Z= 0.264 Chirality : 0.043 0.179 3699 Planarity : 0.003 0.038 4286 Dihedral : 5.881 56.836 3285 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.69 % Allowed : 10.46 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.16), residues: 2961 helix: 1.93 (0.17), residues: 931 sheet: -0.01 (0.23), residues: 531 loop : -0.21 (0.17), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 592 TYR 0.014 0.001 TYR A 636 PHE 0.025 0.001 PHE B 139 TRP 0.014 0.001 TRP A 706 HIS 0.002 0.000 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00276 (24548) covalent geometry : angle 0.49735 (33264) SS BOND : bond 0.00193 ( 2) SS BOND : angle 1.33400 ( 4) hydrogen bonds : bond 0.03849 ( 1109) hydrogen bonds : angle 4.72826 ( 3213) *********************** 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 325 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 253 time to evaluate : 0.795 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: 0.7290 (mtp) cc_final: 0.6958 (mtt) REVERT: A 15 ASN cc_start: 0.7799 (t0) cc_final: 0.7538 (t0) REVERT: A 315 ASN cc_start: 0.8000 (m110) cc_final: 0.7767 (m110) REVERT: A 345 LEU cc_start: 0.8373 (mm) cc_final: 0.8124 (mt) REVERT: A 497 ASP cc_start: 0.8012 (t0) cc_final: 0.7745 (t0) REVERT: A 500 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: B 176 TYR cc_start: 0.7908 (p90) cc_final: 0.7566 (p90) REVERT: B 1003 LYS cc_start: 0.8825 (tptt) cc_final: 0.8545 (tttp) REVERT: B 1154 TYR cc_start: 0.8431 (m-80) cc_final: 0.8197 (m-80) outliers start: 72 outliers final: 49 residues processed: 305 average time/residue: 0.1489 time to fit residues: 74.5221 Evaluate side-chains 284 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 215 THR 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 632 ILE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 738 ASN 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 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 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 452 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 586 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 923 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 240 optimal weight: 20.0000 chunk 265 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 266 optimal weight: 8.9990 chunk 185 optimal weight: 0.0370 chunk 4 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 227 HIS A 412 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN A1115 ASN B 320 ASN ** B 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 ASN ** B1149 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 = 0.3883 r_free = 0.3883 target = 0.120557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.090749 restraints weight = 54078.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089171 restraints weight = 43425.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.089766 restraints weight = 36711.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090213 restraints weight = 32590.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090241 restraints weight = 28579.371| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 24550 Z= 0.285 Angle : 0.622 14.428 33268 Z= 0.328 Chirality : 0.046 0.201 3699 Planarity : 0.004 0.041 4286 Dihedral : 6.119 56.204 3277 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.59 % Allowed : 11.47 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.16), residues: 2961 helix: 1.38 (0.17), residues: 935 sheet: -0.24 (0.23), residues: 514 loop : -0.41 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 827 TYR 0.023 0.002 TYR B 873 PHE 0.023 0.002 PHE A 585 TRP 0.012 0.002 TRP B 641 HIS 0.004 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00665 (24548) covalent geometry : angle 0.62197 (33264) SS BOND : bond 0.00227 ( 2) SS BOND : angle 1.63539 ( 4) hydrogen bonds : bond 0.04489 ( 1109) hydrogen bonds : angle 5.03301 ( 3213) *********************** 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 323 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 227 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7398 (mtp) cc_final: 0.7107 (mtt) REVERT: A 5 ASN cc_start: 0.8727 (p0) cc_final: 0.8527 (p0) REVERT: A 15 ASN cc_start: 0.7956 (t0) cc_final: 0.7689 (t0) REVERT: A 106 MET cc_start: 0.7183 (mtt) cc_final: 0.6918 (mtt) REVERT: A 315 ASN cc_start: 0.8005 (m110) cc_final: 0.7769 (m110) REVERT: A 352 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7249 (m-30) REVERT: A 497 ASP cc_start: 0.8025 (t0) cc_final: 0.7778 (t0) REVERT: A 500 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7286 (mp10) REVERT: A 732 MET cc_start: 0.7619 (mmm) cc_final: 0.7392 (tpt) REVERT: A 978 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7845 (mp) REVERT: A 1209 LEU cc_start: 0.8214 (tp) cc_final: 0.7831 (tt) REVERT: B 127 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7633 (p0) REVERT: B 176 TYR cc_start: 0.8014 (p90) cc_final: 0.7689 (p90) REVERT: B 923 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6568 (mt) REVERT: B 1151 MET cc_start: 0.4713 (pmm) cc_final: 0.4226 (pmm) REVERT: B 1154 TYR cc_start: 0.8471 (m-80) cc_final: 0.8258 (m-80) outliers start: 96 outliers final: 68 residues processed: 299 average time/residue: 0.1444 time to fit residues: 71.2388 Evaluate side-chains 288 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 215 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 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 360 VAL 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 708 GLU Chi-restraints excluded: chain A residue 767 ASP 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 978 LEU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1174 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 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 251 THR 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 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 586 ILE 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 702 ILE 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 923 LEU Chi-restraints excluded: chain B residue 954 VAL Chi-restraints excluded: chain B residue 977 ASN 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 89 optimal weight: 0.8980 chunk 293 optimal weight: 40.0000 chunk 108 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 chunk 274 optimal weight: 10.0000 chunk 159 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN A 912 ASN A1026 ASN A1038 GLN B 320 ASN B 707 GLN ** C 601 ASN ** 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 = 0.3920 r_free = 0.3920 target = 0.122969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093321 restraints weight = 52905.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.091776 restraints weight = 40186.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092145 restraints weight = 36033.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092635 restraints weight = 31525.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093117 restraints weight = 29264.588| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24550 Z= 0.143 Angle : 0.511 11.176 33268 Z= 0.273 Chirality : 0.043 0.184 3699 Planarity : 0.003 0.038 4286 Dihedral : 5.767 55.959 3270 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.18 % Allowed : 12.56 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.16), residues: 2961 helix: 1.68 (0.17), residues: 933 sheet: -0.16 (0.23), residues: 520 loop : -0.34 (0.17), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 48 TYR 0.015 0.001 TYR A 636 PHE 0.019 0.001 PHE A 464 TRP 0.014 0.001 TRP A 706 HIS 0.002 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00328 (24548) covalent geometry : angle 0.51011 (33264) SS BOND : bond 0.00619 ( 2) SS BOND : angle 3.04556 ( 4) hydrogen bonds : bond 0.03909 ( 1109) hydrogen bonds : angle 4.76547 ( 3213) *********************** 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 315 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 230 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7285 (mtp) cc_final: 0.6976 (mtt) REVERT: A 5 ASN cc_start: 0.8703 (p0) cc_final: 0.8477 (p0) REVERT: A 15 ASN cc_start: 0.7901 (t0) cc_final: 0.7654 (t0) REVERT: A 34 LYS cc_start: 0.8008 (tttt) cc_final: 0.7661 (tttm) REVERT: A 106 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6967 (mtt) REVERT: A 315 ASN cc_start: 0.7957 (m110) cc_final: 0.7740 (m110) REVERT: A 345 LEU cc_start: 0.8404 (mm) cc_final: 0.8185 (mt) REVERT: A 428 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7038 (tp) REVERT: A 497 ASP cc_start: 0.8101 (t0) cc_final: 0.7775 (t0) REVERT: A 500 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: A 732 MET cc_start: 0.7538 (mmm) cc_final: 0.7332 (tpt) REVERT: A 978 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 1209 LEU cc_start: 0.8230 (tp) cc_final: 0.7834 (tt) REVERT: B 127 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7666 (p0) REVERT: B 176 TYR cc_start: 0.7977 (p90) cc_final: 0.7628 (p90) REVERT: B 1003 LYS cc_start: 0.8871 (tptt) cc_final: 0.8611 (tttp) REVERT: B 1151 MET cc_start: 0.4752 (pmm) cc_final: 0.4238 (pmm) REVERT: B 1154 TYR cc_start: 0.8454 (m-80) cc_final: 0.8154 (m-80) REVERT: C 377 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8135 (pt) outliers start: 85 outliers final: 62 residues processed: 298 average time/residue: 0.1327 time to fit residues: 66.1977 Evaluate side-chains 290 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 106 MET 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 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 977 SER Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 1026 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 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 251 THR 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 500 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 586 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 904 ASP 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 368 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 ILE 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 77 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN A 412 ASN A 470 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN B 320 ASN ** B1149 ASN ** 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 = 0.3906 r_free = 0.3906 target = 0.122053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092193 restraints weight = 53577.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091045 restraints weight = 42715.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.091355 restraints weight = 35699.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.091848 restraints weight = 31309.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091883 restraints weight = 28840.563| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1486 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= 0.186 Angle : 0.540 14.309 33268 Z= 0.286 Chirality : 0.044 0.193 3699 Planarity : 0.003 0.037 4286 Dihedral : 5.749 55.893 3268 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.51 % Allowed : 13.12 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.16), residues: 2961 helix: 1.62 (0.17), residues: 933 sheet: -0.17 (0.23), residues: 520 loop : -0.41 (0.17), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1023 TYR 0.018 0.001 TYR B 873 PHE 0.022 0.001 PHE A 464 TRP 0.009 0.001 TRP B 559 HIS 0.003 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00431 (24548) covalent geometry : angle 0.53978 (33264) SS BOND : bond 0.00251 ( 2) SS BOND : angle 2.44335 ( 4) hydrogen bonds : bond 0.03991 ( 1109) hydrogen bonds : angle 4.77757 ( 3213) *********************** 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 324 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 230 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7280 (mtp) cc_final: 0.6979 (mtt) REVERT: A 5 ASN cc_start: 0.8727 (p0) cc_final: 0.8504 (p0) REVERT: A 15 ASN cc_start: 0.7902 (t0) cc_final: 0.7654 (t0) REVERT: A 34 LYS cc_start: 0.8029 (tttt) cc_final: 0.7641 (tttm) REVERT: A 315 ASN cc_start: 0.7913 (m110) cc_final: 0.7696 (m110) REVERT: A 352 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7096 (m-30) REVERT: A 497 ASP cc_start: 0.8097 (t0) cc_final: 0.7805 (t0) REVERT: A 500 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: A 673 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7623 (tp) REVERT: A 732 MET cc_start: 0.7608 (mmm) cc_final: 0.6755 (mmm) REVERT: A 978 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7811 (mp) REVERT: A 1209 LEU cc_start: 0.8228 (tp) cc_final: 0.7853 (tt) REVERT: B 127 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7719 (p0) REVERT: B 176 TYR cc_start: 0.7992 (p90) cc_final: 0.7648 (p90) REVERT: B 1003 LYS cc_start: 0.8877 (tptt) cc_final: 0.8628 (tttp) REVERT: B 1151 MET cc_start: 0.4677 (pmm) cc_final: 0.4148 (pmm) REVERT: B 1154 TYR cc_start: 0.8415 (m-80) cc_final: 0.8148 (m-80) REVERT: C 377 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8080 (pt) outliers start: 94 outliers final: 73 residues processed: 303 average time/residue: 0.1356 time to fit residues: 68.7514 Evaluate side-chains 302 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 223 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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 469 ASP 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 673 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 767 ASP 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 978 LEU 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 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 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 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 586 ILE 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 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 1113 ILE 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 377 LEU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 556 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 263 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 470 ASN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN A 912 ASN B 320 ASN B 769 GLN ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** 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 = 0.3894 r_free = 0.3894 target = 0.121283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.090902 restraints weight = 53655.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.090084 restraints weight = 41544.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.090562 restraints weight = 36236.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.091084 restraints weight = 31711.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.091148 restraints weight = 27387.538| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24550 Z= 0.224 Angle : 0.577 13.540 33268 Z= 0.303 Chirality : 0.045 0.188 3699 Planarity : 0.003 0.038 4286 Dihedral : 5.856 56.100 3268 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.33 % Allowed : 13.86 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.16), residues: 2961 helix: 1.48 (0.17), residues: 935 sheet: -0.19 (0.23), residues: 502 loop : -0.46 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1017 TYR 0.020 0.002 TYR B 873 PHE 0.021 0.002 PHE A 464 TRP 0.010 0.001 TRP B 641 HIS 0.004 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00521 (24548) covalent geometry : angle 0.57631 (33264) SS BOND : bond 0.00268 ( 2) SS BOND : angle 2.20847 ( 4) hydrogen bonds : bond 0.04134 ( 1109) hydrogen bonds : angle 4.82945 ( 3213) *********************** 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 310 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 221 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7291 (mtp) cc_final: 0.6898 (mtt) REVERT: A 5 ASN cc_start: 0.8743 (p0) cc_final: 0.8533 (p0) REVERT: A 15 ASN cc_start: 0.7897 (t0) cc_final: 0.7672 (t0) REVERT: A 34 LYS cc_start: 0.8017 (tttt) cc_final: 0.7623 (tttm) REVERT: A 315 ASN cc_start: 0.7927 (m110) cc_final: 0.7697 (m110) REVERT: A 345 LEU cc_start: 0.8384 (mm) cc_final: 0.8175 (mt) REVERT: A 352 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7119 (m-30) REVERT: A 428 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7148 (tp) REVERT: A 497 ASP cc_start: 0.8101 (t0) cc_final: 0.7746 (t0) REVERT: A 500 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7149 (mp10) REVERT: A 673 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7651 (tp) REVERT: A 1209 LEU cc_start: 0.8237 (tp) cc_final: 0.8016 (tp) REVERT: B 127 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7707 (p0) REVERT: B 176 TYR cc_start: 0.8002 (p90) cc_final: 0.7685 (p90) REVERT: B 1151 MET cc_start: 0.4725 (pmm) cc_final: 0.4173 (pmm) REVERT: B 1154 TYR cc_start: 0.8430 (m-80) cc_final: 0.8185 (m-80) REVERT: C 377 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8098 (pt) outliers start: 89 outliers final: 73 residues processed: 292 average time/residue: 0.1393 time to fit residues: 67.7499 Evaluate side-chains 298 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 219 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 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 767 ASP 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 1174 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 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 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 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 586 ILE 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 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 377 LEU 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 188 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 151 optimal weight: 0.9990 chunk 242 optimal weight: 20.0000 chunk 177 optimal weight: 1.9990 chunk 283 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 288 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 470 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN C 484 ASN ** 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 = 0.3922 r_free = 0.3922 target = 0.123065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093330 restraints weight = 53191.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.092259 restraints weight = 42079.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092796 restraints weight = 33637.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093303 restraints weight = 29820.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093250 restraints weight = 27992.297| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1640 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= 0.136 Angle : 0.525 12.174 33268 Z= 0.277 Chirality : 0.043 0.194 3699 Planarity : 0.003 0.037 4286 Dihedral : 5.726 56.166 3268 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.99 % Allowed : 14.28 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.16), residues: 2961 helix: 1.73 (0.17), residues: 933 sheet: -0.07 (0.23), residues: 514 loop : -0.43 (0.17), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 48 TYR 0.015 0.001 TYR A 636 PHE 0.023 0.001 PHE A 464 TRP 0.012 0.001 TRP A 706 HIS 0.003 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00312 (24548) covalent geometry : angle 0.52441 (33264) SS BOND : bond 0.00184 ( 2) SS BOND : angle 1.53787 ( 4) hydrogen bonds : bond 0.03790 ( 1109) hydrogen bonds : angle 4.67844 ( 3213) *********************** 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 313 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 233 time to evaluate : 1.131 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: 0.7281 (mtp) cc_final: 0.6871 (mtt) REVERT: A 5 ASN cc_start: 0.8719 (p0) cc_final: 0.8512 (p0) REVERT: A 15 ASN cc_start: 0.7815 (t0) cc_final: 0.7601 (t0) REVERT: A 106 MET cc_start: 0.7175 (mmm) cc_final: 0.6911 (mtt) REVERT: A 345 LEU cc_start: 0.8348 (mm) cc_final: 0.8131 (mt) REVERT: A 352 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7064 (m-30) REVERT: A 428 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7177 (tp) REVERT: A 500 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7170 (mp10) REVERT: A 673 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7599 (tp) REVERT: A 1082 LYS cc_start: 0.7982 (ptmm) cc_final: 0.7746 (ptmm) REVERT: B 127 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7702 (p0) REVERT: B 176 TYR cc_start: 0.7960 (p90) cc_final: 0.7618 (p90) REVERT: B 724 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7308 (p) REVERT: B 1003 LYS cc_start: 0.8886 (tptt) cc_final: 0.8647 (tttp) REVERT: B 1151 MET cc_start: 0.4508 (pmm) cc_final: 0.3968 (pmm) REVERT: B 1154 TYR cc_start: 0.8423 (m-80) cc_final: 0.8134 (m-80) outliers start: 80 outliers final: 68 residues processed: 299 average time/residue: 0.1426 time to fit residues: 71.1871 Evaluate side-chains 293 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 219 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 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 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 1020 THR 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 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 452 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 533 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 591 ASN 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 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 262 optimal weight: 40.0000 chunk 131 optimal weight: 0.9980 chunk 245 optimal weight: 10.0000 chunk 148 optimal weight: 0.3980 chunk 174 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 292 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN A 412 ASN A 470 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** 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 = 0.3928 r_free = 0.3928 target = 0.123453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.096503 restraints weight = 53276.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093621 restraints weight = 45082.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093901 restraints weight = 42563.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.094166 restraints weight = 38282.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.094174 restraints weight = 35353.488| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24550 Z= 0.131 Angle : 0.528 15.079 33268 Z= 0.278 Chirality : 0.043 0.191 3699 Planarity : 0.003 0.037 4286 Dihedral : 5.648 56.311 3268 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.91 % Allowed : 14.42 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.16), residues: 2961 helix: 1.79 (0.17), residues: 934 sheet: -0.03 (0.23), residues: 513 loop : -0.41 (0.17), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1192 TYR 0.019 0.001 TYR A 502 PHE 0.022 0.001 PHE A 464 TRP 0.010 0.001 TRP A 706 HIS 0.002 0.000 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00301 (24548) covalent geometry : angle 0.52621 (33264) SS BOND : bond 0.00162 ( 2) SS BOND : angle 3.56255 ( 4) hydrogen bonds : bond 0.03718 ( 1109) hydrogen bonds : angle 4.62973 ( 3213) *********************** 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 302 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 224 time to evaluate : 0.965 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: 0.7279 (mtp) cc_final: 0.6869 (mtt) REVERT: A 5 ASN cc_start: 0.8709 (p0) cc_final: 0.8490 (p0) REVERT: A 34 LYS cc_start: 0.7956 (tttt) cc_final: 0.7572 (tttm) REVERT: A 345 LEU cc_start: 0.8332 (mm) cc_final: 0.8109 (mt) REVERT: A 352 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7043 (m-30) REVERT: A 428 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7032 (tp) REVERT: A 500 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: A 673 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7565 (tp) REVERT: A 1082 LYS cc_start: 0.8012 (ptmm) cc_final: 0.7780 (ptmm) REVERT: B 127 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7662 (p0) REVERT: B 176 TYR cc_start: 0.7939 (p90) cc_final: 0.7589 (p90) REVERT: B 901 TYR cc_start: 0.6628 (OUTLIER) cc_final: 0.6394 (m-80) REVERT: B 1003 LYS cc_start: 0.8837 (tptt) cc_final: 0.8599 (tttp) REVERT: B 1151 MET cc_start: 0.4566 (pmm) cc_final: 0.4006 (pmm) outliers start: 78 outliers final: 67 residues processed: 287 average time/residue: 0.1400 time to fit residues: 67.4335 Evaluate side-chains 294 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 221 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 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 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 1020 THR Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1184 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 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 452 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 533 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 591 ASN 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 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 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 58 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 37 optimal weight: 0.0070 chunk 207 optimal weight: 0.5980 chunk 295 optimal weight: 10.0000 chunk 289 optimal weight: 50.0000 chunk 246 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 470 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 ASN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 GLN ** 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 = 0.3937 r_free = 0.3937 target = 0.124093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095642 restraints weight = 53388.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095013 restraints weight = 51250.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.096082 restraints weight = 40661.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.096133 restraints weight = 31811.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.096262 restraints weight = 31109.860| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1763 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= 0.122 Angle : 0.529 14.846 33268 Z= 0.277 Chirality : 0.043 0.193 3699 Planarity : 0.003 0.038 4286 Dihedral : 5.586 56.517 3268 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.80 % Allowed : 14.80 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.16), residues: 2961 helix: 1.78 (0.17), residues: 946 sheet: -0.00 (0.23), residues: 509 loop : -0.42 (0.17), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 48 TYR 0.020 0.001 TYR A 502 PHE 0.021 0.001 PHE A 464 TRP 0.011 0.001 TRP A 706 HIS 0.003 0.000 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00278 (24548) covalent geometry : angle 0.52849 (33264) SS BOND : bond 0.00480 ( 2) SS BOND : angle 2.94819 ( 4) hydrogen bonds : bond 0.03645 ( 1109) hydrogen bonds : angle 4.56471 ( 3213) ********************** 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 305 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 230 time to evaluate : 0.820 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: 0.7296 (mtp) cc_final: 0.6869 (mtt) REVERT: A 5 ASN cc_start: 0.8689 (p0) cc_final: 0.8450 (p0) REVERT: A 34 LYS cc_start: 0.7881 (tttt) cc_final: 0.7510 (tttm) REVERT: A 345 LEU cc_start: 0.8341 (mm) cc_final: 0.8099 (mt) REVERT: A 352 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6983 (m-30) REVERT: A 428 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7106 (tp) REVERT: A 497 ASP cc_start: 0.8113 (t0) cc_final: 0.7852 (t0) REVERT: A 500 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: A 673 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7558 (tp) REVERT: A 1134 MET cc_start: 0.7802 (mmm) cc_final: 0.7533 (tpt) REVERT: B 127 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7565 (p0) REVERT: B 176 TYR cc_start: 0.7936 (p90) cc_final: 0.7595 (p90) REVERT: B 1003 LYS cc_start: 0.8864 (tptt) cc_final: 0.8638 (tttp) REVERT: B 1151 MET cc_start: 0.4313 (pmm) cc_final: 0.3876 (pmm) outliers start: 75 outliers final: 65 residues processed: 290 average time/residue: 0.1375 time to fit residues: 67.0100 Evaluate side-chains 291 residues out of total 2725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 221 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 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 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 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 1020 THR Chi-restraints excluded: chain A residue 1148 ILE 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 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 452 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 533 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 591 ASN 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 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 904 ASP Chi-restraints excluded: chain B residue 912 ILE Chi-restraints excluded: chain B residue 923 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 1144 TRP 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 152 optimal weight: 0.4980 chunk 227 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 276 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 470 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN ** B 470 ASN ** 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 = 0.3914 r_free = 0.3914 target = 0.122651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.093933 restraints weight = 53334.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.092599 restraints weight = 53171.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093448 restraints weight = 42578.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094468 restraints weight = 35516.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.094531 restraints weight = 29903.552| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24550 Z= 0.181 Angle : 0.559 15.033 33268 Z= 0.293 Chirality : 0.044 0.189 3699 Planarity : 0.003 0.037 4286 Dihedral : 5.575 56.578 3264 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.84 % Allowed : 14.72 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.16), residues: 2961 helix: 1.65 (0.17), residues: 942 sheet: -0.19 (0.22), residues: 534 loop : -0.44 (0.17), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.019 0.001 TYR B 901 PHE 0.023 0.001 PHE A 464 TRP 0.010 0.001 TRP B 559 HIS 0.004 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00419 (24548) covalent geometry : angle 0.55793 (33264) SS BOND : bond 0.00410 ( 2) SS BOND : angle 2.79541 ( 4) hydrogen bonds : bond 0.03853 ( 1109) hydrogen bonds : angle 4.65034 ( 3213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3522.15 seconds wall clock time: 62 minutes 11.69 seconds (3731.69 seconds total)