Starting phenix.real_space_refine on Mon Sep 30 15:09:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu8_29455/09_2024/8fu8_29455_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu8_29455/09_2024/8fu8_29455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu8_29455/09_2024/8fu8_29455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu8_29455/09_2024/8fu8_29455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu8_29455/09_2024/8fu8_29455_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu8_29455/09_2024/8fu8_29455_neut.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 109 5.16 5 C 16192 2.51 5 N 4177 2.21 5 O 4991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25469 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 8183 Classifications: {'peptide': 1046} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 989} Chain breaks: 4 Chain: "B" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8360 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 55, 'TRANS': 1013} Chain breaks: 2 Chain: "C" Number of atoms: 8211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8211 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 53, 'TRANS': 996} Chain breaks: 5 Chain: "A" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 253 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 224 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 238 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 16.76, per 1000 atoms: 0.66 Number of scatterers: 25469 At special positions: 0 Unit cell: (137.313, 155.621, 163.111, 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 109 16.00 O 4991 8.00 N 4177 7.00 C 16192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Links applied NAG-ASN " NAG A1206 " - " ASN A 225 " " NAG A1215 " - " ASN A1082 " " NAG B1210 " - " ASN B 61 " " NAG C1204 " - " ASN C 225 " " NAG C1212 " - " ASN C 315 " Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 3.3 seconds 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5920 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 42 sheets defined 23.8% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.529A pdb=" N TRP A 337 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 370 through 373 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 742 through 767 removed outlier: 3.532A pdb=" N ASP A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 810 Processing helix chain 'A' and resid 850 through 869 Processing helix chain 'A' and resid 870 through 874 Processing helix chain 'A' and resid 881 through 892 Processing helix chain 'A' and resid 896 through 902 removed outlier: 4.132A pdb=" N LEU A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 925 Processing helix chain 'A' and resid 929 through 949 removed outlier: 3.946A pdb=" N VAL A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 952 No H-bonds generated for 'chain 'A' and resid 950 through 952' Processing helix chain 'A' and resid 960 through 966 Processing helix chain 'A' and resid 969 through 1017 removed outlier: 4.295A pdb=" N VAL A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'B' and resid 277 through 287 removed outlier: 4.051A pdb=" N SER B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.931A pdb=" N TRP B 337 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.292A pdb=" N ASN B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.655A pdb=" N VAL B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 727 Processing helix chain 'B' and resid 730 through 737 Processing helix chain 'B' and resid 738 through 741 Processing helix chain 'B' and resid 742 through 767 removed outlier: 3.751A pdb=" N ASP B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 810 Processing helix chain 'B' and resid 850 through 869 Processing helix chain 'B' and resid 870 through 874 Processing helix chain 'B' and resid 881 through 891 Processing helix chain 'B' and resid 896 through 902 removed outlier: 4.185A pdb=" N LEU B 900 " --> pdb=" O THR B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 923 removed outlier: 3.802A pdb=" N ILE B 918 " --> pdb=" O ALA B 914 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN B 919 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 920 " --> pdb=" O GLY B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 949 removed outlier: 3.894A pdb=" N VAL B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 969 through 1017 removed outlier: 3.897A pdb=" N VAL B 975 " --> pdb=" O PRO B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1130 removed outlier: 3.670A pdb=" N LEU B1129 " --> pdb=" O LEU B1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 288 Processing helix chain 'C' and resid 348 through 354 removed outlier: 4.097A pdb=" N LEU C 352 " --> pdb=" O ASP C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 373 Processing helix chain 'C' and resid 721 through 727 Processing helix chain 'C' and resid 730 through 738 removed outlier: 4.227A pdb=" N LEU C 736 " --> pdb=" O GLU C 732 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 741 No H-bonds generated for 'chain 'C' and resid 739 through 741' Processing helix chain 'C' and resid 742 through 767 removed outlier: 3.809A pdb=" N ASP C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 810 Processing helix chain 'C' and resid 850 through 868 Processing helix chain 'C' and resid 870 through 874 Processing helix chain 'C' and resid 881 through 892 Processing helix chain 'C' and resid 896 through 902 removed outlier: 4.277A pdb=" N LEU C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 923 Processing helix chain 'C' and resid 925 through 928 Processing helix chain 'C' and resid 929 through 949 removed outlier: 3.949A pdb=" N VAL C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 952 No H-bonds generated for 'chain 'C' and resid 950 through 952' Processing helix chain 'C' and resid 960 through 968 Processing helix chain 'C' and resid 970 through 1017 removed outlier: 3.876A pdb=" N VAL C 975 " --> pdb=" O PRO C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1130 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.883A pdb=" N ASN A 61 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TYR A 253 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER A 196 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 36 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.757A pdb=" N ASP A 271 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 295 through 300 removed outlier: 6.951A pdb=" N VAL A 579 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 312 removed outlier: 4.782A pdb=" N GLU A 308 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP A 558 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE A 549 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 338 through 342 removed outlier: 3.642A pdb=" N VAL A 379 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS A 345 " --> pdb=" O CYS A 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 338 through 342 removed outlier: 3.642A pdb=" N VAL A 379 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN A 378 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU A 500 " --> pdb=" O ASN A 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 436 through 437 removed outlier: 4.589A pdb=" N LEU A 436 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 639 removed outlier: 6.587A pdb=" N ILE A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 685 through 688 removed outlier: 6.571A pdb=" N ALA A 685 " --> pdb=" O ILE B 772 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LYS B 774 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASN A 687 " --> pdb=" O LYS B 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 695 through 698 removed outlier: 3.740A pdb=" N ALA A1062 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 712 removed outlier: 5.866A pdb=" N TYR A1051 " --> pdb=" O HIS A1032 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS A1032 " --> pdb=" O TYR A1051 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 720 removed outlier: 4.164A pdb=" N LYS A 717 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 771 through 774 Processing sheet with id=AB7, first strand: chain 'A' and resid 1104 through 1109 removed outlier: 4.904A pdb=" N ALA A1071 " --> pdb=" O SER A1107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 7.874A pdb=" N ASN B 61 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TYR B 253 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER B 196 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.515A pdb=" N THR B 258 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP B 274 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU B 260 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B 272 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS B 262 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.509A pdb=" N PHE B 159 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 295 through 303 removed outlier: 5.379A pdb=" N ILE B 296 " --> pdb=" O THR B 583 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR B 583 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN B 298 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 581 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 300 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 578 " --> pdb=" O GLN B 597 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 312 removed outlier: 5.227A pdb=" N ASP B 558 " --> pdb=" O ILE B 571 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA B 559 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B 549 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 338 through 342 removed outlier: 6.586A pdb=" N CYS B 345 " --> pdb=" O CYS B 509 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 338 through 342 removed outlier: 5.432A pdb=" N ASN B 378 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU B 500 " --> pdb=" O ASN B 378 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 638 through 639 removed outlier: 6.604A pdb=" N ILE B 654 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 686 through 688 Processing sheet with id=AC8, first strand: chain 'B' and resid 695 through 712 removed outlier: 6.560A pdb=" N SER B 695 " --> pdb=" O THR B1060 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR B1060 " --> pdb=" O SER B 695 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 697 " --> pdb=" O ASN B1058 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN B1058 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLU B1056 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR B1051 " --> pdb=" O HIS B1032 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS B1032 " --> pdb=" O TYR B1051 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 695 through 712 removed outlier: 6.560A pdb=" N SER B 695 " --> pdb=" O THR B1060 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR B1060 " --> pdb=" O SER B 695 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 697 " --> pdb=" O ASN B1058 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN B1058 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLU B1056 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B1062 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE B1079 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN B1090 " --> pdb=" O GLU B1095 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLU B1095 " --> pdb=" O GLN B1090 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 720 removed outlier: 4.269A pdb=" N LYS B 717 " --> pdb=" O LEU B 845 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1104 through 1109 removed outlier: 4.785A pdb=" N ALA B1071 " --> pdb=" O SER B1107 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.546A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ASN C 61 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR C 253 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE C 192 " --> pdb=" O ASP C 219 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP C 219 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 194 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.367A pdb=" N THR C 258 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP C 274 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 260 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA C 272 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS C 262 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 159 through 163 removed outlier: 3.890A pdb=" N GLY C 103 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 178 through 180 Processing sheet with id=AD7, first strand: chain 'C' and resid 295 through 303 removed outlier: 5.209A pdb=" N ILE C 296 " --> pdb=" O THR C 583 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR C 583 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLN C 298 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL C 581 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY C 578 " --> pdb=" O GLN C 597 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 308 through 312 removed outlier: 3.961A pdb=" N GLU C 308 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 338 through 342 removed outlier: 3.901A pdb=" N VAL C 379 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N CYS C 345 " --> pdb=" O CYS C 509 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 338 through 342 removed outlier: 3.901A pdb=" N VAL C 379 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASN C 378 " --> pdb=" O GLU C 500 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU C 500 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 492 " --> pdb=" O ILE C 386 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 638 through 639 removed outlier: 6.576A pdb=" N ILE C 654 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 695 through 712 removed outlier: 7.045A pdb=" N GLN C1055 " --> pdb=" O THR C 700 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE C 702 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE C 704 " --> pdb=" O TYR C1051 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR C1051 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 706 " --> pdb=" O VAL C1049 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C1049 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR C 708 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU C1047 " --> pdb=" O THR C 708 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE C 710 " --> pdb=" O VAL C1045 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL C1045 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY C1043 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR C1051 " --> pdb=" O HIS C1032 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N HIS C1032 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 695 through 712 removed outlier: 7.045A pdb=" N GLN C1055 " --> pdb=" O THR C 700 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE C 702 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE C 704 " --> pdb=" O TYR C1051 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR C1051 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 706 " --> pdb=" O VAL C1049 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C1049 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR C 708 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU C1047 " --> pdb=" O THR C 708 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE C 710 " --> pdb=" O VAL C1045 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL C1045 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY C1043 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C1062 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 717 through 720 removed outlier: 4.381A pdb=" N LYS C 717 " --> pdb=" O LEU C 845 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1104 through 1109 removed outlier: 6.100A pdb=" N ALA C1071 " --> pdb=" O SER C1107 " (cutoff:3.500A) 1030 hydrogen bonds defined for protein. 2787 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.26 Time building geometry restraints manager: 7.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4972 1.32 - 1.45: 6444 1.45 - 1.57: 14481 1.57 - 1.69: 17 1.69 - 1.82: 139 Bond restraints: 26053 Sorted by residual: bond pdb=" C1 NAG B1203 " pdb=" O1 NAG B1203 " ideal model delta sigma weight residual 1.376 1.483 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C1 NAG B1204 " pdb=" O1 NAG B1204 " ideal model delta sigma weight residual 1.376 1.482 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C1 NAG C1215 " pdb=" O1 NAG C1215 " ideal model delta sigma weight residual 1.376 1.481 -0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C1 NAG A1211 " pdb=" O1 NAG A1211 " ideal model delta sigma weight residual 1.376 1.481 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C1 NAG C1213 " pdb=" O1 NAG C1213 " ideal model delta sigma weight residual 1.376 1.481 -0.105 2.00e-02 2.50e+03 2.75e+01 ... (remaining 26048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 32074 2.00 - 4.01: 2813 4.01 - 6.01: 460 6.01 - 8.01: 132 8.01 - 10.02: 5 Bond angle restraints: 35484 Sorted by residual: angle pdb=" C LEU C 207 " pdb=" N PRO C 208 " pdb=" CA PRO C 208 " ideal model delta sigma weight residual 119.56 128.29 -8.73 1.02e+00 9.61e-01 7.33e+01 angle pdb=" C LEU C 845 " pdb=" N PRO C 846 " pdb=" CA PRO C 846 " ideal model delta sigma weight residual 119.66 125.70 -6.04 7.20e-01 1.93e+00 7.04e+01 angle pdb=" C PRO A 25 " pdb=" N PRO A 26 " pdb=" CA PRO A 26 " ideal model delta sigma weight residual 120.31 128.42 -8.11 9.80e-01 1.04e+00 6.84e+01 angle pdb=" C LEU A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta sigma weight residual 120.21 128.06 -7.85 9.60e-01 1.09e+00 6.69e+01 angle pdb=" C THR A 775 " pdb=" N PRO A 776 " pdb=" CA PRO A 776 " ideal model delta sigma weight residual 119.66 125.45 -5.79 7.20e-01 1.93e+00 6.46e+01 ... (remaining 35479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 15529 17.96 - 35.92: 457 35.92 - 53.88: 100 53.88 - 71.84: 42 71.84 - 89.80: 17 Dihedral angle restraints: 16145 sinusoidal: 6935 harmonic: 9210 Sorted by residual: dihedral pdb=" CA THR B 583 " pdb=" C THR B 583 " pdb=" N PRO B 584 " pdb=" CA PRO B 584 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR C 583 " pdb=" C THR C 583 " pdb=" N PRO C 584 " pdb=" CA PRO C 584 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER C 367 " pdb=" C SER C 367 " pdb=" N PRO C 368 " pdb=" CA PRO C 368 " ideal model delta harmonic sigma weight residual 180.00 163.45 16.55 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 16142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.987: 4139 0.987 - 1.975: 0 1.975 - 2.962: 0 2.962 - 3.949: 0 3.949 - 4.937: 1 Chirality restraints: 4140 Sorted by residual: chirality pdb=" C1 NAG A1206 " pdb=" ND2 ASN A 225 " pdb=" C2 NAG A1206 " pdb=" O5 NAG A1206 " both_signs ideal model delta sigma weight residual False -2.40 2.54 -4.94 2.00e-01 2.50e+01 6.09e+02 chirality pdb=" CG LEU C 233 " pdb=" CB LEU C 233 " pdb=" CD1 LEU C 233 " pdb=" CD2 LEU C 233 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" C2 NAG C1204 " pdb=" C1 NAG C1204 " pdb=" C3 NAG C1204 " pdb=" N2 NAG C1204 " both_signs ideal model delta sigma weight residual False -2.49 -2.85 0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 4137 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 437 " 0.039 2.00e-02 2.50e+03 2.11e-02 8.90e+00 pdb=" CG TYR A 437 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 437 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 437 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 437 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 437 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 437 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 437 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 474 " 0.032 2.00e-02 2.50e+03 1.98e-02 6.86e+00 pdb=" CG PHE C 474 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE C 474 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 474 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE C 474 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 474 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 474 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 407 " 0.032 2.00e-02 2.50e+03 1.66e-02 5.51e+00 pdb=" CG TYR B 407 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR B 407 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 407 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 407 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 407 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 407 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 407 " 0.022 2.00e-02 2.50e+03 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 8712 2.85 - 3.36: 22932 3.36 - 3.87: 42590 3.87 - 4.39: 49334 4.39 - 4.90: 82283 Nonbonded interactions: 205851 Sorted by model distance: nonbonded pdb=" NZ LYS A 541 " pdb=" OD2 ASP A 558 " model vdw 2.336 3.120 nonbonded pdb=" OE2 GLU B 709 " pdb=" NZ LYS B1012 " model vdw 2.340 3.120 nonbonded pdb=" ND2 ASN B 590 " pdb=" OH TYR B 658 " model vdw 2.344 3.120 nonbonded pdb=" NZ LYS C 428 " pdb=" O PHE C 481 " model vdw 2.358 3.120 nonbonded pdb=" NZ LYS A 838 " pdb=" OD1 ASP C 558 " model vdw 2.384 3.120 ... (remaining 205846 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 66 or resid 81 through 233 or resid 247 through \ 606 or resid 616 through 1130 or resid 1201 through 1203 or (resid 1204 and (na \ me C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name \ C8 or name N2 or name O3 or name O4 or name O5 or name O6 or name O7 )) or resid \ 1205 through 1209 or (resid 1210 and (name C1 or name C2 or name C3 or name C4 \ or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or \ name O5 or name O6 or name O7 )) or resid 1211 or (resid 1212 and (name C1 or na \ me C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ N2 or name O3 or name O4 or name O5 or name O6 or name O7 )) or resid 1213 throu \ gh 1215)) selection = (chain 'B' and (resid 25 through 66 or resid 81 through 233 or resid 247 through \ 606 or resid 616 through 1130 or resid 1201 through 1203 or (resid 1204 and (na \ me C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name \ C8 or name N2 or name O3 or name O4 or name O5 or name O6 or name O7 )) or resid \ 1205 or (resid 1206 and (name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or na \ me O6 or name O7 )) or resid 1207 through 1211 or (resid 1212 and (name C1 or na \ me C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ N2 or name O3 or name O4 or name O5 or name O6 or name O7 )) or resid 1213 throu \ gh 1214 or (resid 1215 and (name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or \ name O6 or name O7 )))) selection = (chain 'C' and (resid 25 through 233 or resid 247 through 811 or resid 838 throu \ gh 1130 or resid 1201 through 1205 or (resid 1206 and (name C1 or name C2 or nam \ e C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O \ 3 or name O4 or name O5 or name O6 or name O7 )) or resid 1207 through 1209 or ( \ resid 1210 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ r name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or name O6 or n \ ame O7 )) or resid 1211 through 1214 or (resid 1215 and (name C1 or name C2 or n \ ame C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name N2 or name \ O3 or name O4 or name O5 or name O6 or name O7 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.900 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: 0.030 Extract box with map and model: 1.140 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 61.920 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 0.013 0.112 26053 Z= 0.859 Angle : 1.290 10.018 35484 Z= 0.864 Chirality : 0.111 4.937 4140 Planarity : 0.005 0.033 4525 Dihedral : 10.271 89.798 10225 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 1.05 % Allowed : 5.36 % Favored : 93.59 % Rotamer: Outliers : 0.14 % Allowed : 0.51 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3137 helix: 0.33 (0.19), residues: 658 sheet: 0.70 (0.19), residues: 625 loop : -0.82 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.005 TRP A 64 HIS 0.005 0.001 HIS A 137 PHE 0.032 0.003 PHE C 474 TYR 0.039 0.004 TYR A 437 ARG 0.005 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 503 time to evaluate : 2.671 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 90 VAL cc_start: 0.8635 (t) cc_final: 0.8310 (p) REVERT: A 167 LEU cc_start: 0.7189 (mt) cc_final: 0.6859 (mm) REVERT: A 191 TYR cc_start: 0.6777 (m-80) cc_final: 0.6454 (m-80) REVERT: A 387 ARG cc_start: 0.6332 (ttt180) cc_final: 0.5492 (mpt180) REVERT: A 401 LYS cc_start: 0.7271 (pttt) cc_final: 0.7071 (ptmm) REVERT: A 435 TYR cc_start: 0.6479 (m-80) cc_final: 0.6234 (m-80) REVERT: A 443 SER cc_start: 0.7631 (p) cc_final: 0.7323 (p) REVERT: A 445 LEU cc_start: 0.6563 (tp) cc_final: 0.6071 (tp) REVERT: A 641 ASN cc_start: 0.7397 (t0) cc_final: 0.7105 (t0) REVERT: A 729 ASP cc_start: 0.7534 (p0) cc_final: 0.7138 (p0) REVERT: A 842 LEU cc_start: 0.8296 (tp) cc_final: 0.7935 (mt) REVERT: A 1122 TYR cc_start: 0.7719 (t80) cc_final: 0.7308 (m-10) REVERT: B 28 TYR cc_start: 0.7287 (m-80) cc_final: 0.7075 (m-80) REVERT: B 144 MET cc_start: 0.2138 (ttm) cc_final: 0.1574 (tpt) REVERT: C 63 THR cc_start: 0.7975 (m) cc_final: 0.7695 (p) REVERT: C 315 ASN cc_start: 0.5811 (OUTLIER) cc_final: 0.5464 (p0) REVERT: C 318 ASN cc_start: 0.7191 (m-40) cc_final: 0.6940 (t0) REVERT: C 353 TYR cc_start: 0.7035 (t80) cc_final: 0.6819 (t80) REVERT: C 411 ASP cc_start: 0.6882 (m-30) cc_final: 0.6433 (m-30) REVERT: C 448 PHE cc_start: 0.7845 (m-80) cc_final: 0.7615 (m-80) REVERT: C 492 TYR cc_start: 0.6662 (m-80) cc_final: 0.5858 (m-10) REVERT: C 1025 ASP cc_start: 0.7269 (m-30) cc_final: 0.7049 (m-30) outliers start: 4 outliers final: 1 residues processed: 507 average time/residue: 0.4112 time to fit residues: 314.8289 Evaluate side-chains 245 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 243 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain C residue 315 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 0.9990 chunk 238 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 246 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 286 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 139 ASN A 198 HIS A 209 GLN A 354 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN A1085 HIS B 66 HIS B 693 ASN B1058 ASN C 187 ASN C 266 ASN C 490 GLN C1032 HIS ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26053 Z= 0.209 Angle : 0.643 13.068 35484 Z= 0.344 Chirality : 0.049 1.064 4140 Planarity : 0.004 0.047 4525 Dihedral : 5.656 51.420 4535 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.61 % Favored : 94.23 % Rotamer: Outliers : 1.12 % Allowed : 5.23 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3137 helix: 1.70 (0.21), residues: 649 sheet: 0.67 (0.18), residues: 715 loop : -1.00 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 420 HIS 0.008 0.001 HIS B 137 PHE 0.025 0.002 PHE B 159 TYR 0.026 0.002 TYR C 161 ARG 0.007 0.001 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 290 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6282 (m-40) cc_final: 0.6062 (m-40) REVERT: A 90 VAL cc_start: 0.8586 (t) cc_final: 0.8135 (p) REVERT: A 137 HIS cc_start: 0.4499 (OUTLIER) cc_final: 0.4194 (p-80) REVERT: A 162 VAL cc_start: 0.8213 (t) cc_final: 0.7804 (p) REVERT: A 386 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7984 (tp) REVERT: A 435 TYR cc_start: 0.6802 (m-80) cc_final: 0.6416 (m-80) REVERT: A 641 ASN cc_start: 0.7481 (t0) cc_final: 0.7140 (t0) REVERT: A 729 ASP cc_start: 0.7632 (p0) cc_final: 0.7352 (p0) REVERT: A 842 LEU cc_start: 0.8336 (tp) cc_final: 0.7964 (mt) REVERT: A 1122 TYR cc_start: 0.7753 (t80) cc_final: 0.7467 (m-10) REVERT: B 28 TYR cc_start: 0.7346 (m-80) cc_final: 0.7117 (m-80) REVERT: B 144 MET cc_start: 0.1994 (ttm) cc_final: 0.1447 (tpt) REVERT: B 917 LYS cc_start: 0.8819 (mttt) cc_final: 0.8585 (mtmm) REVERT: B 972 GLU cc_start: 0.7157 (mp0) cc_final: 0.6924 (mp0) REVERT: B 1058 ASN cc_start: 0.7072 (p0) cc_final: 0.6865 (p0) REVERT: B 1128 GLU cc_start: 0.7424 (tp30) cc_final: 0.7192 (mm-30) REVERT: C 63 THR cc_start: 0.8007 (m) cc_final: 0.7761 (p) REVERT: C 120 VAL cc_start: 0.7995 (t) cc_final: 0.7749 (m) REVERT: C 324 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7175 (tm-30) REVERT: C 448 PHE cc_start: 0.7928 (m-80) cc_final: 0.7604 (m-80) REVERT: C 489 TYR cc_start: 0.3018 (OUTLIER) cc_final: 0.1586 (m-80) REVERT: C 492 TYR cc_start: 0.6697 (m-80) cc_final: 0.6035 (m-10) REVERT: C 566 LEU cc_start: 0.8078 (mp) cc_final: 0.7817 (mp) outliers start: 31 outliers final: 14 residues processed: 310 average time/residue: 0.3631 time to fit residues: 181.3253 Evaluate side-chains 229 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 212 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 729 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 286 optimal weight: 0.0010 chunk 309 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 229 optimal weight: 8.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS A 209 GLN A 315 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN A 885 GLN ** A1032 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 587 ASN B 994 GLN C 125 ASN C 202 ASN C 266 ASN C 639 HIS ** C1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26053 Z= 0.228 Angle : 0.597 10.706 35484 Z= 0.315 Chirality : 0.045 0.457 4140 Planarity : 0.004 0.043 4525 Dihedral : 5.600 48.906 4533 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.41 % Favored : 93.40 % Rotamer: Outliers : 1.41 % Allowed : 6.78 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3137 helix: 1.79 (0.21), residues: 655 sheet: 0.57 (0.18), residues: 732 loop : -1.11 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 617 HIS 0.017 0.001 HIS B 66 PHE 0.027 0.002 PHE B 159 TYR 0.025 0.002 TYR B1051 ARG 0.007 0.000 ARG C 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 225 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: A 387 ARG cc_start: 0.6189 (ttt180) cc_final: 0.5502 (mpt180) REVERT: A 435 TYR cc_start: 0.6851 (m-80) cc_final: 0.6566 (m-80) REVERT: A 729 ASP cc_start: 0.7565 (p0) cc_final: 0.7224 (p0) REVERT: A 792 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5603 (p0) REVERT: A 842 LEU cc_start: 0.8415 (tp) cc_final: 0.8009 (mp) REVERT: A 900 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8451 (tt) REVERT: B 144 MET cc_start: 0.1811 (ttm) cc_final: 0.1325 (tpt) REVERT: B 1058 ASN cc_start: 0.7438 (p0) cc_final: 0.7228 (p0) REVERT: B 1128 GLU cc_start: 0.7416 (tp30) cc_final: 0.7150 (mm-30) REVERT: C 63 THR cc_start: 0.8041 (m) cc_final: 0.7718 (p) REVERT: C 120 VAL cc_start: 0.7943 (t) cc_final: 0.7675 (m) REVERT: C 324 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7179 (tm-30) REVERT: C 489 TYR cc_start: 0.3248 (OUTLIER) cc_final: 0.1788 (m-80) REVERT: C 566 LEU cc_start: 0.8038 (mp) cc_final: 0.7816 (mp) outliers start: 39 outliers final: 24 residues processed: 257 average time/residue: 0.3559 time to fit residues: 149.8113 Evaluate side-chains 217 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 1016 CYS Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 337 TRP Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 729 ASP Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN ** A1032 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS B 639 HIS B 885 GLN C1082 ASN ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26053 Z= 0.291 Angle : 0.612 9.940 35484 Z= 0.320 Chirality : 0.046 0.424 4140 Planarity : 0.004 0.042 4525 Dihedral : 5.644 47.912 4533 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.66 % Favored : 93.18 % Rotamer: Outliers : 1.48 % Allowed : 7.80 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3137 helix: 1.66 (0.21), residues: 670 sheet: 0.37 (0.19), residues: 726 loop : -1.29 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 870 HIS 0.006 0.001 HIS B 639 PHE 0.023 0.002 PHE C 384 TYR 0.024 0.002 TYR B1051 ARG 0.005 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 203 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7998 (m-10) REVERT: A 168 MET cc_start: 0.6874 (mpp) cc_final: 0.6417 (mpp) REVERT: A 225 ASN cc_start: 0.6689 (OUTLIER) cc_final: 0.6466 (m-40) REVERT: A 387 ARG cc_start: 0.6079 (ttt180) cc_final: 0.5375 (mpt180) REVERT: A 401 LYS cc_start: 0.7544 (mmtp) cc_final: 0.7307 (mmtp) REVERT: A 435 TYR cc_start: 0.6906 (m-80) cc_final: 0.6631 (m-80) REVERT: A 446 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7193 (mtpp) REVERT: A 701 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8760 (t0) REVERT: A 729 ASP cc_start: 0.7619 (p0) cc_final: 0.7294 (p0) REVERT: B 52 GLN cc_start: 0.7832 (tp40) cc_final: 0.7572 (tp40) REVERT: B 144 MET cc_start: 0.1829 (ttm) cc_final: 0.1463 (tpt) REVERT: B 1128 GLU cc_start: 0.7410 (tp30) cc_final: 0.7121 (mm-30) REVERT: C 63 THR cc_start: 0.8080 (m) cc_final: 0.7668 (p) REVERT: C 120 VAL cc_start: 0.7918 (t) cc_final: 0.7630 (m) REVERT: C 324 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7166 (tm-30) REVERT: C 489 TYR cc_start: 0.3587 (OUTLIER) cc_final: 0.2150 (m-80) REVERT: C 492 TYR cc_start: 0.6324 (m-80) cc_final: 0.6073 (m-10) REVERT: C 566 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7987 (mp) outliers start: 41 outliers final: 26 residues processed: 234 average time/residue: 0.3438 time to fit residues: 133.7184 Evaluate side-chains 209 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 1016 CYS Chi-restraints excluded: chain C residue 337 TRP Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 729 ASP Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 259 optimal weight: 8.9990 chunk 210 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 273 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A1032 HIS B 693 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN C 597 GLN C 898 ASN ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 26053 Z= 0.428 Angle : 0.675 9.287 35484 Z= 0.351 Chirality : 0.049 0.251 4140 Planarity : 0.005 0.042 4525 Dihedral : 6.367 50.465 4533 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.76 % Rotamer: Outliers : 1.91 % Allowed : 8.52 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3137 helix: 1.57 (0.21), residues: 654 sheet: 0.18 (0.19), residues: 684 loop : -1.44 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 870 HIS 0.007 0.001 HIS B1042 PHE 0.028 0.002 PHE B 159 TYR 0.025 0.002 TYR B1051 ARG 0.006 0.001 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 196 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.8144 (m-10) REVERT: A 168 MET cc_start: 0.7039 (mpp) cc_final: 0.6439 (mpp) REVERT: A 387 ARG cc_start: 0.5936 (ttt180) cc_final: 0.5234 (mpt180) REVERT: A 446 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7439 (mtpp) REVERT: A 729 ASP cc_start: 0.7712 (p0) cc_final: 0.7334 (p0) REVERT: B 144 MET cc_start: 0.1605 (ttm) cc_final: 0.1402 (tpt) REVERT: B 1128 GLU cc_start: 0.7286 (tp30) cc_final: 0.7062 (mm-30) REVERT: C 63 THR cc_start: 0.8091 (m) cc_final: 0.7625 (p) REVERT: C 120 VAL cc_start: 0.7961 (t) cc_final: 0.7749 (m) REVERT: C 489 TYR cc_start: 0.4000 (OUTLIER) cc_final: 0.2430 (m-80) REVERT: C 492 TYR cc_start: 0.6472 (m-80) cc_final: 0.6107 (m-10) REVERT: C 566 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.8019 (mp) outliers start: 53 outliers final: 41 residues processed: 236 average time/residue: 0.3517 time to fit residues: 138.7010 Evaluate side-chains 221 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 176 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 587 ASN Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 969 ASP Chi-restraints excluded: chain B residue 1016 CYS Chi-restraints excluded: chain B residue 1102 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 729 ASP Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 885 GLN Chi-restraints excluded: chain C residue 1016 CYS Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 0.9980 chunk 274 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 304 optimal weight: 1.9990 chunk 253 optimal weight: 0.2980 chunk 141 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 ASN C 597 GLN C 701 ASN C1085 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26053 Z= 0.163 Angle : 0.547 9.275 35484 Z= 0.288 Chirality : 0.044 0.291 4140 Planarity : 0.004 0.042 4525 Dihedral : 5.545 48.608 4533 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.85 % Favored : 93.02 % Rotamer: Outliers : 1.55 % Allowed : 9.49 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3137 helix: 2.02 (0.21), residues: 646 sheet: 0.17 (0.19), residues: 707 loop : -1.37 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 337 HIS 0.004 0.001 HIS B 137 PHE 0.027 0.001 PHE B 159 TYR 0.024 0.001 TYR B 136 ARG 0.011 0.000 ARG C 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6953 (mpp) cc_final: 0.6341 (mpp) REVERT: A 225 ASN cc_start: 0.6506 (OUTLIER) cc_final: 0.6177 (m-40) REVERT: A 387 ARG cc_start: 0.6011 (ttt180) cc_final: 0.5097 (mmp-170) REVERT: A 401 LYS cc_start: 0.7600 (mmtp) cc_final: 0.7377 (mmtp) REVERT: A 446 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7362 (mtpp) REVERT: A 505 PRO cc_start: 0.7467 (Cg_endo) cc_final: 0.7226 (Cg_exo) REVERT: A 729 ASP cc_start: 0.7658 (p0) cc_final: 0.7288 (p0) REVERT: A 900 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8429 (tt) REVERT: B 52 GLN cc_start: 0.7757 (tp40) cc_final: 0.7530 (tp40) REVERT: B 1128 GLU cc_start: 0.7217 (tp30) cc_final: 0.6975 (mm-30) REVERT: C 63 THR cc_start: 0.7984 (m) cc_final: 0.7655 (p) REVERT: C 120 VAL cc_start: 0.7939 (t) cc_final: 0.7703 (m) REVERT: C 448 PHE cc_start: 0.7884 (m-80) cc_final: 0.7572 (m-80) REVERT: C 489 TYR cc_start: 0.3635 (OUTLIER) cc_final: 0.2119 (m-80) REVERT: C 492 TYR cc_start: 0.6475 (m-80) cc_final: 0.6184 (m-10) outliers start: 43 outliers final: 24 residues processed: 235 average time/residue: 0.3563 time to fit residues: 136.7967 Evaluate side-chains 202 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 587 ASN Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 1102 ASP Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26053 Z= 0.239 Angle : 0.568 10.334 35484 Z= 0.296 Chirality : 0.045 0.259 4140 Planarity : 0.004 0.041 4525 Dihedral : 5.539 49.551 4533 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.14 % Favored : 92.73 % Rotamer: Outliers : 1.80 % Allowed : 9.74 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3137 helix: 2.00 (0.21), residues: 654 sheet: 0.11 (0.19), residues: 675 loop : -1.41 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 870 HIS 0.004 0.001 HIS B 137 PHE 0.028 0.002 PHE B 159 TYR 0.021 0.001 TYR B1051 ARG 0.008 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 179 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6946 (mpp) cc_final: 0.6376 (mpp) REVERT: A 225 ASN cc_start: 0.6518 (OUTLIER) cc_final: 0.6164 (m-40) REVERT: A 401 LYS cc_start: 0.7593 (mmtp) cc_final: 0.7358 (mmtp) REVERT: A 446 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7437 (mtpp) REVERT: A 505 PRO cc_start: 0.7391 (Cg_endo) cc_final: 0.7169 (Cg_exo) REVERT: A 729 ASP cc_start: 0.7670 (p0) cc_final: 0.7289 (p0) REVERT: A 900 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8440 (tt) REVERT: B 52 GLN cc_start: 0.7766 (tp40) cc_final: 0.7524 (tp40) REVERT: B 1128 GLU cc_start: 0.7213 (tp30) cc_final: 0.6971 (mm-30) REVERT: C 63 THR cc_start: 0.8034 (m) cc_final: 0.7652 (p) REVERT: C 120 VAL cc_start: 0.7943 (t) cc_final: 0.7702 (m) REVERT: C 324 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7141 (tm-30) REVERT: C 448 PHE cc_start: 0.7869 (m-80) cc_final: 0.7511 (m-80) REVERT: C 489 TYR cc_start: 0.3768 (OUTLIER) cc_final: 0.2234 (m-80) REVERT: C 492 TYR cc_start: 0.6609 (m-80) cc_final: 0.6193 (m-10) outliers start: 50 outliers final: 31 residues processed: 218 average time/residue: 0.3420 time to fit residues: 123.3583 Evaluate side-chains 207 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 587 ASN Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 1102 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 1016 CYS Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 59 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 150 optimal weight: 20.0000 chunk 28 optimal weight: 0.3980 chunk 238 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26053 Z= 0.183 Angle : 0.539 9.864 35484 Z= 0.282 Chirality : 0.044 0.253 4140 Planarity : 0.004 0.041 4525 Dihedral : 5.189 49.614 4533 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.20 % Favored : 92.67 % Rotamer: Outliers : 1.55 % Allowed : 10.03 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3137 helix: 2.13 (0.21), residues: 652 sheet: 0.13 (0.19), residues: 670 loop : -1.39 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.005 0.001 HIS B 137 PHE 0.026 0.001 PHE B 159 TYR 0.027 0.001 TYR B 136 ARG 0.008 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 187 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.6185 (t) cc_final: 0.5915 (m) REVERT: A 168 MET cc_start: 0.6761 (mpp) cc_final: 0.6189 (mpp) REVERT: A 390 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7140 (mp0) REVERT: A 401 LYS cc_start: 0.7618 (mmtp) cc_final: 0.7397 (mmtp) REVERT: A 446 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7420 (mtpp) REVERT: A 451 ASP cc_start: 0.6401 (t0) cc_final: 0.6133 (t70) REVERT: A 729 ASP cc_start: 0.7678 (p0) cc_final: 0.7285 (p0) REVERT: A 900 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8408 (tt) REVERT: B 52 GLN cc_start: 0.7734 (tp40) cc_final: 0.7495 (tp40) REVERT: B 1128 GLU cc_start: 0.7184 (tp30) cc_final: 0.6919 (mm-30) REVERT: C 63 THR cc_start: 0.7968 (m) cc_final: 0.7657 (p) REVERT: C 120 VAL cc_start: 0.7912 (t) cc_final: 0.7670 (m) REVERT: C 448 PHE cc_start: 0.7873 (m-80) cc_final: 0.7540 (m-80) REVERT: C 489 TYR cc_start: 0.3701 (OUTLIER) cc_final: 0.2203 (m-80) REVERT: C 492 TYR cc_start: 0.6631 (m-80) cc_final: 0.6154 (m-10) outliers start: 43 outliers final: 30 residues processed: 224 average time/residue: 0.2757 time to fit residues: 102.8574 Evaluate side-chains 210 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 1102 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 885 GLN Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 0.6980 chunk 290 optimal weight: 0.2980 chunk 265 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 255 optimal weight: 0.6980 chunk 267 optimal weight: 1.9990 chunk 281 optimal weight: 0.0770 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26053 Z= 0.159 Angle : 0.524 10.156 35484 Z= 0.274 Chirality : 0.043 0.252 4140 Planarity : 0.004 0.041 4525 Dihedral : 4.910 48.991 4533 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.92 % Favored : 92.96 % Rotamer: Outliers : 1.37 % Allowed : 10.32 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3137 helix: 2.22 (0.21), residues: 653 sheet: 0.13 (0.19), residues: 668 loop : -1.34 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 420 HIS 0.004 0.001 HIS C 66 PHE 0.024 0.001 PHE B 159 TYR 0.019 0.001 TYR B1051 ARG 0.006 0.000 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.6169 (t) cc_final: 0.5903 (m) REVERT: A 168 MET cc_start: 0.6919 (mpp) cc_final: 0.6322 (mpp) REVERT: A 225 ASN cc_start: 0.6539 (OUTLIER) cc_final: 0.6161 (m-40) REVERT: A 390 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7090 (mp0) REVERT: A 446 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7369 (mtpp) REVERT: A 729 ASP cc_start: 0.7649 (p0) cc_final: 0.7257 (p0) REVERT: A 900 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8385 (tt) REVERT: B 52 GLN cc_start: 0.7730 (tp40) cc_final: 0.7497 (tp40) REVERT: B 96 GLU cc_start: 0.5911 (mm-30) cc_final: 0.5495 (mm-30) REVERT: B 1128 GLU cc_start: 0.7142 (tp30) cc_final: 0.6866 (mm-30) REVERT: C 63 THR cc_start: 0.7977 (m) cc_final: 0.7695 (p) REVERT: C 120 VAL cc_start: 0.7816 (t) cc_final: 0.7591 (m) REVERT: C 448 PHE cc_start: 0.7820 (m-80) cc_final: 0.7460 (m-80) REVERT: C 489 TYR cc_start: 0.3600 (OUTLIER) cc_final: 0.2147 (m-80) REVERT: C 492 TYR cc_start: 0.6674 (m-80) cc_final: 0.6243 (m-10) outliers start: 38 outliers final: 28 residues processed: 225 average time/residue: 0.3515 time to fit residues: 133.0208 Evaluate side-chains 212 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 885 GLN Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 313 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 249 optimal weight: 0.0970 chunk 25 optimal weight: 0.3980 chunk 193 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26053 Z= 0.226 Angle : 0.549 11.131 35484 Z= 0.286 Chirality : 0.044 0.242 4140 Planarity : 0.004 0.060 4525 Dihedral : 5.047 50.208 4533 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.11 % Favored : 92.80 % Rotamer: Outliers : 1.37 % Allowed : 10.39 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3137 helix: 2.14 (0.21), residues: 654 sheet: 0.07 (0.19), residues: 669 loop : -1.36 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 337 HIS 0.004 0.001 HIS B 137 PHE 0.029 0.002 PHE B 159 TYR 0.026 0.001 TYR B 136 ARG 0.006 0.000 ARG C 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.6138 (t) cc_final: 0.5846 (m) REVERT: A 168 MET cc_start: 0.6818 (mpp) cc_final: 0.6229 (mpp) REVERT: A 225 ASN cc_start: 0.6612 (OUTLIER) cc_final: 0.6229 (m-40) REVERT: A 390 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7101 (mp0) REVERT: A 446 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7372 (mtpp) REVERT: A 505 PRO cc_start: 0.7372 (Cg_endo) cc_final: 0.7038 (Cg_exo) REVERT: A 729 ASP cc_start: 0.7668 (p0) cc_final: 0.7291 (p0) REVERT: A 900 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8411 (tt) REVERT: B 52 GLN cc_start: 0.7751 (tp40) cc_final: 0.7506 (tp40) REVERT: B 96 GLU cc_start: 0.5906 (mm-30) cc_final: 0.5476 (mm-30) REVERT: B 1128 GLU cc_start: 0.7179 (tp30) cc_final: 0.6897 (mm-30) REVERT: C 63 THR cc_start: 0.7999 (m) cc_final: 0.7653 (p) REVERT: C 120 VAL cc_start: 0.7900 (t) cc_final: 0.7670 (m) REVERT: C 448 PHE cc_start: 0.7848 (m-80) cc_final: 0.7470 (m-80) REVERT: C 489 TYR cc_start: 0.3660 (OUTLIER) cc_final: 0.2181 (m-80) REVERT: C 492 TYR cc_start: 0.6687 (m-80) cc_final: 0.6319 (m-10) outliers start: 38 outliers final: 28 residues processed: 213 average time/residue: 0.3491 time to fit residues: 123.7965 Evaluate side-chains 208 residues out of total 2771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 840 ASN Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 104 optimal weight: 0.0870 chunk 257 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.151714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097840 restraints weight = 38320.107| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.45 r_work: 0.2994 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26053 Z= 0.162 Angle : 0.530 10.938 35484 Z= 0.277 Chirality : 0.043 0.239 4140 Planarity : 0.004 0.059 4525 Dihedral : 4.883 49.818 4533 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.01 % Favored : 92.92 % Rotamer: Outliers : 1.37 % Allowed : 10.43 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3137 helix: 2.24 (0.21), residues: 651 sheet: 0.11 (0.19), residues: 677 loop : -1.34 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 337 HIS 0.003 0.001 HIS B 137 PHE 0.029 0.001 PHE B 159 TYR 0.026 0.001 TYR A1122 ARG 0.006 0.000 ARG C 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5556.32 seconds wall clock time: 102 minutes 20.40 seconds (6140.40 seconds total)