Starting phenix.real_space_refine on Thu Feb 15 03:51:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsq_30164/02_2024/7bsq_30164_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsq_30164/02_2024/7bsq_30164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsq_30164/02_2024/7bsq_30164.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsq_30164/02_2024/7bsq_30164.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsq_30164/02_2024/7bsq_30164_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bsq_30164/02_2024/7bsq_30164_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 7117 2.51 5 N 1807 2.21 5 O 2033 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 637": "OE1" <-> "OE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A ARG 839": "NH1" <-> "NH2" Residue "A TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A PHE 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A GLU 1081": "OE1" <-> "OE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C ARG 309": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11024 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8311 Classifications: {'peptide': 1028} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 1002} Chain breaks: 3 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.28, per 1000 atoms: 0.57 Number of scatterers: 11024 At special positions: 0 Unit cell: (106.24, 87.15, 161.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 58 16.00 P 2 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 2033 8.00 N 1807 7.00 C 7117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM10990 O3A ADP A1102 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-3 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 404 " - " ASN C 294 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 2.2 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 8 sheets defined 38.6% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 56 through 63 removed outlier: 4.104A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 81 removed outlier: 3.500A pdb=" N TYR A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 122 Proline residue: A 94 - end of helix removed outlier: 3.630A pdb=" N VAL A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 191 through 194 No H-bonds generated for 'chain 'A' and resid 191 through 194' Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 287 through 311 removed outlier: 3.575A pdb=" N THR A 301 " --> pdb=" O PHE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 359 through 370 removed outlier: 3.586A pdb=" N LYS A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 410 through 413 No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 496 through 507 removed outlier: 3.629A pdb=" N ALA A 500 " --> pdb=" O PRO A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 575 through 590 removed outlier: 4.230A pdb=" N GLU A 579 " --> pdb=" O HIS A 576 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS A 582 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 619 removed outlier: 3.652A pdb=" N ARG A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 633 removed outlier: 3.859A pdb=" N VAL A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 710 through 720 removed outlier: 3.970A pdb=" N ARG A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 760 Processing helix chain 'A' and resid 771 through 781 removed outlier: 3.783A pdb=" N LYS A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 802 removed outlier: 3.826A pdb=" N VAL A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 823 through 826 No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 841 through 844 No H-bonds generated for 'chain 'A' and resid 841 through 844' Processing helix chain 'A' and resid 854 through 892 removed outlier: 3.906A pdb=" N HIS A 864 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU A 865 " --> pdb=" O ALA A 861 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 878 " --> pdb=" O VAL A 874 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Proline residue: A 887 - end of helix removed outlier: 4.121A pdb=" N GLN A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 913 removed outlier: 5.105A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 925 removed outlier: 3.787A pdb=" N LEU A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 937 No H-bonds generated for 'chain 'A' and resid 934 through 937' Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 953 through 977 removed outlier: 3.894A pdb=" N PHE A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1012 Processing helix chain 'A' and resid 1020 through 1041 removed outlier: 3.709A pdb=" N PHE A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1062 removed outlier: 4.048A pdb=" N SER A1062 " --> pdb=" O ALA A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1089 Proline residue: A1080 - end of helix removed outlier: 4.087A pdb=" N LEU A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A1086 " --> pdb=" O ILE A1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 51 through 73 Proline residue: C 63 - end of helix removed outlier: 3.898A pdb=" N PHE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 93 removed outlier: 4.219A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 93' Processing helix chain 'C' and resid 132 through 135 No H-bonds generated for 'chain 'C' and resid 132 through 135' Processing helix chain 'C' and resid 140 through 143 No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 147 through 150 No H-bonds generated for 'chain 'C' and resid 147 through 150' Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 223 through 226 No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.873A pdb=" N PHE C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 20 through 22 Processing sheet with id= B, first strand: chain 'A' and resid 124 through 128 removed outlier: 3.608A pdb=" N LYS A 136 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 146 through 150 removed outlier: 6.889A pdb=" N VAL A 260 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 161 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.906A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 250 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 847 through 849 removed outlier: 3.553A pdb=" N VAL A 829 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR A 405 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE A 814 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 407 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS A 669 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR A 408 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TRP A 671 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 785 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TYR A 747 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N LEU A 786 " --> pdb=" O TYR A 747 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 749 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU A 696 " --> pdb=" O GLY A 748 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE A 750 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 698 " --> pdb=" O ILE A 750 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 420 through 426 removed outlier: 3.686A pdb=" N ALA A 647 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N CYS A 424 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA A 645 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE A 426 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ILE A 643 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 598 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA A 645 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 596 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 647 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG A 594 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 603 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 558 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS A 536 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS A 552 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 534 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 78 through 81 removed outlier: 3.676A pdb=" N ARG C 309 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 104 through 110 removed outlier: 4.770A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1916 1.32 - 1.45: 3064 1.45 - 1.57: 6205 1.57 - 1.70: 3 1.70 - 1.83: 91 Bond restraints: 11279 Sorted by residual: bond pdb=" CA PHE A 64 " pdb=" C PHE A 64 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.34e-02 5.57e+03 4.01e+01 bond pdb=" C4 ADP A1102 " pdb=" C5 ADP A1102 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.797 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.790 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.49e+01 ... (remaining 11274 not shown) Histogram of bond angle deviations from ideal: 88.55 - 106.62: 287 106.62 - 124.69: 14808 124.69 - 142.77: 195 142.77 - 160.84: 0 160.84 - 178.91: 2 Bond angle restraints: 15292 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 178.17 -69.49 3.00e+00 1.11e-01 5.36e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 178.91 -69.28 3.00e+00 1.11e-01 5.33e+02 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 88.55 21.66 3.00e+00 1.11e-01 5.22e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.02 89.82 19.20 3.00e+00 1.11e-01 4.09e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.69 90.79 18.90 3.00e+00 1.11e-01 3.97e+01 ... (remaining 15287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 6216 23.97 - 47.95: 474 47.95 - 71.92: 64 71.92 - 95.90: 11 95.90 - 119.87: 2 Dihedral angle restraints: 6767 sinusoidal: 2798 harmonic: 3969 Sorted by residual: dihedral pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " pdb=" SG CYS C 102 " pdb=" CB CYS C 102 " ideal model delta sinusoidal sigma weight residual -86.00 -20.89 -65.11 1 1.00e+01 1.00e-02 5.56e+01 dihedral pdb=" O2A ADP A1102 " pdb=" O3A ADP A1102 " pdb=" PA ADP A1102 " pdb=" PB ADP A1102 " ideal model delta sinusoidal sigma weight residual -60.00 59.87 -119.87 1 2.00e+01 2.50e-03 3.60e+01 dihedral pdb=" C5' ADP A1102 " pdb=" O5' ADP A1102 " pdb=" PA ADP A1102 " pdb=" O2A ADP A1102 " ideal model delta sinusoidal sigma weight residual -60.00 -174.15 114.15 1 2.00e+01 2.50e-03 3.38e+01 ... (remaining 6764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1672 0.125 - 0.250: 50 0.250 - 0.376: 3 0.376 - 0.501: 1 0.501 - 0.626: 1 Chirality restraints: 1727 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.82e+01 chirality pdb=" C1 MAN B 3 " pdb=" O3 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.27 0.13 2.00e-02 2.50e+03 4.07e+01 chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.80e+00 ... (remaining 1724 not shown) Planarity restraints: 1921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 404 " -0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG C 404 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 404 " -0.097 2.00e-02 2.50e+03 pdb=" N2 NAG C 404 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG C 404 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 405 " -0.293 2.00e-02 2.50e+03 2.54e-01 8.09e+02 pdb=" C7 NAG C 405 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG C 405 " -0.008 2.00e-02 2.50e+03 pdb=" N2 NAG C 405 " 0.441 2.00e-02 2.50e+03 pdb=" O7 NAG C 405 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.077 2.00e-02 2.50e+03 6.50e-02 5.28e+01 pdb=" C7 NAG B 2 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.023 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.104 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.062 2.00e-02 2.50e+03 ... (remaining 1918 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 105 2.45 - 3.06: 8348 3.06 - 3.68: 15393 3.68 - 4.29: 25879 4.29 - 4.90: 43640 Nonbonded interactions: 93365 Sorted by model distance: nonbonded pdb=" O2A ADP A1102 " pdb="MG MG A1104 " model vdw 1.841 2.170 nonbonded pdb=" F4 ALF A1101 " pdb=" O1B ADP A1102 " model vdw 1.866 2.390 nonbonded pdb=" CA GLY A 815 " pdb="MG MG A1103 " model vdw 1.878 2.570 nonbonded pdb=" O ILE A 225 " pdb=" CB ALA A 236 " model vdw 1.895 3.460 nonbonded pdb=" OG SER A 813 " pdb=" OG SER A 827 " model vdw 1.897 2.440 ... (remaining 93360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.070 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 33.070 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.014 0.112 11279 Z= 0.893 Angle : 1.301 69.486 15292 Z= 0.596 Chirality : 0.061 0.626 1727 Planarity : 0.011 0.306 1919 Dihedral : 16.724 119.870 4196 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 35.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.95 % Favored : 83.98 % Rotamer: Outliers : 6.31 % Allowed : 17.28 % Favored : 76.41 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.29 (0.18), residues: 1342 helix: -3.17 (0.16), residues: 568 sheet: -2.32 (0.34), residues: 203 loop : -4.30 (0.20), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP C 260 HIS 0.006 0.002 HIS C 131 PHE 0.034 0.003 PHE A 971 TYR 0.032 0.003 TYR C 297 ARG 0.004 0.001 ARG A 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 176 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.6854 (OUTLIER) cc_final: 0.6605 (p90) REVERT: A 135 ARG cc_start: 0.7455 (ptm-80) cc_final: 0.7198 (ttp80) REVERT: A 181 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6787 (mt-10) REVERT: A 292 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8249 (mp) REVERT: A 330 LYS cc_start: 0.8254 (tttt) cc_final: 0.8017 (tttm) REVERT: A 340 MET cc_start: 0.7631 (mtp) cc_final: 0.7417 (mtt) REVERT: A 492 ILE cc_start: 0.8530 (pt) cc_final: 0.8170 (pt) REVERT: A 521 ARG cc_start: 0.5989 (mtt180) cc_final: 0.5585 (mtp85) REVERT: A 628 LYS cc_start: 0.8423 (ttmt) cc_final: 0.7430 (tptt) REVERT: A 943 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.4847 (tpt) REVERT: C 69 PHE cc_start: 0.8634 (t80) cc_final: 0.8410 (t80) REVERT: C 210 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8288 (tttp) outliers start: 76 outliers final: 56 residues processed: 239 average time/residue: 0.2605 time to fit residues: 85.0189 Evaluate side-chains 220 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 160 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 633 PHE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 846 ASP Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 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 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 ASN A 59 ASN A 63 GLN A 106 GLN A 114 HIS A 130 ASN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN A 329 GLN A 392 ASN A 397 ASN A 524 ASN A 539 ASN A 574 GLN A 744 HIS A 840 GLN A 888 GLN A1050 GLN C 152 ASN C 347 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11279 Z= 0.231 Angle : 0.891 31.721 15292 Z= 0.402 Chirality : 0.047 0.549 1727 Planarity : 0.005 0.046 1919 Dihedral : 10.711 134.646 1688 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.49 % Allowed : 20.43 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.21), residues: 1342 helix: -1.67 (0.20), residues: 567 sheet: -1.86 (0.36), residues: 201 loop : -3.17 (0.22), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.003 0.001 HIS A 576 PHE 0.024 0.002 PHE A 633 TYR 0.017 0.002 TYR A 876 ARG 0.002 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 181 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.6713 (OUTLIER) cc_final: 0.6505 (p-80) REVERT: A 135 ARG cc_start: 0.7337 (ptm-80) cc_final: 0.7074 (ttp80) REVERT: A 212 GLU cc_start: 0.6979 (tp30) cc_final: 0.6650 (tp30) REVERT: A 330 LYS cc_start: 0.8158 (tttt) cc_final: 0.7911 (tttm) REVERT: A 367 LYS cc_start: 0.8258 (mttt) cc_final: 0.7864 (mtmt) REVERT: A 506 LYS cc_start: 0.7866 (tttt) cc_final: 0.7642 (ttpt) REVERT: A 519 TYR cc_start: 0.7652 (m-10) cc_final: 0.7107 (m-80) REVERT: A 521 ARG cc_start: 0.6316 (mtt180) cc_final: 0.5866 (mtp85) REVERT: A 628 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7324 (tptt) REVERT: A 816 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8440 (p0) REVERT: A 943 MET cc_start: 0.7662 (tpt) cc_final: 0.4753 (tpt) REVERT: A 1055 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7910 (t80) REVERT: A 1075 PHE cc_start: 0.7984 (t80) cc_final: 0.7184 (m-80) REVERT: C 53 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6261 (pt) REVERT: C 69 PHE cc_start: 0.8495 (t80) cc_final: 0.8294 (t80) REVERT: C 275 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8142 (pp) outliers start: 54 outliers final: 30 residues processed: 222 average time/residue: 0.2590 time to fit residues: 79.1382 Evaluate side-chains 197 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN A 828 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11279 Z= 0.297 Angle : 0.864 31.327 15292 Z= 0.387 Chirality : 0.047 0.554 1727 Planarity : 0.004 0.043 1919 Dihedral : 9.710 131.537 1625 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.40 % Allowed : 21.59 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.21), residues: 1342 helix: -1.20 (0.20), residues: 583 sheet: -1.54 (0.37), residues: 199 loop : -2.86 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 323 HIS 0.003 0.001 HIS A 864 PHE 0.023 0.002 PHE A 633 TYR 0.018 0.002 TYR A 876 ARG 0.003 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 180 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.6717 (OUTLIER) cc_final: 0.6500 (p-80) REVERT: A 135 ARG cc_start: 0.7292 (ptm-80) cc_final: 0.7053 (ttp80) REVERT: A 212 GLU cc_start: 0.6957 (tp30) cc_final: 0.6627 (tp30) REVERT: A 330 LYS cc_start: 0.8178 (tttt) cc_final: 0.7921 (tttm) REVERT: A 367 LYS cc_start: 0.8319 (mttt) cc_final: 0.7938 (mtmt) REVERT: A 519 TYR cc_start: 0.7735 (m-10) cc_final: 0.7260 (m-80) REVERT: A 628 LYS cc_start: 0.8229 (ttmt) cc_final: 0.7316 (tptt) REVERT: A 843 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7633 (ptm-80) REVERT: A 943 MET cc_start: 0.7730 (tpt) cc_final: 0.4740 (tpt) REVERT: A 1003 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8514 (tp) REVERT: A 1075 PHE cc_start: 0.8015 (t80) cc_final: 0.7265 (m-80) REVERT: C 161 ARG cc_start: 0.8124 (ttt180) cc_final: 0.7861 (ttp-170) REVERT: C 162 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7128 (ttm110) REVERT: C 275 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8140 (pp) outliers start: 53 outliers final: 37 residues processed: 217 average time/residue: 0.2696 time to fit residues: 80.4007 Evaluate side-chains 203 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 162 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 129 optimal weight: 0.4980 chunk 115 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 54 ASN A 69 ASN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11279 Z= 0.169 Angle : 0.805 29.649 15292 Z= 0.353 Chirality : 0.044 0.500 1727 Planarity : 0.004 0.042 1919 Dihedral : 8.861 126.217 1615 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.90 % Allowed : 22.43 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.23), residues: 1342 helix: -0.46 (0.22), residues: 574 sheet: -1.24 (0.37), residues: 198 loop : -2.49 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.003 0.001 HIS A 114 PHE 0.020 0.001 PHE A 633 TYR 0.014 0.001 TYR A 608 ARG 0.012 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 174 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6786 (tp30) cc_final: 0.6464 (tp30) REVERT: A 256 LYS cc_start: 0.8318 (pttm) cc_final: 0.8104 (pttp) REVERT: A 330 LYS cc_start: 0.8069 (tttt) cc_final: 0.7781 (tttm) REVERT: A 367 LYS cc_start: 0.8264 (mttt) cc_final: 0.7925 (mtmt) REVERT: A 519 TYR cc_start: 0.7698 (m-10) cc_final: 0.7353 (m-80) REVERT: A 521 ARG cc_start: 0.6619 (mtt180) cc_final: 0.6109 (mtp85) REVERT: A 628 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7250 (tptt) REVERT: A 941 LEU cc_start: 0.5507 (OUTLIER) cc_final: 0.5215 (tt) REVERT: A 1075 PHE cc_start: 0.7924 (t80) cc_final: 0.7220 (m-80) REVERT: C 155 LYS cc_start: 0.7881 (pttp) cc_final: 0.7621 (pttt) REVERT: C 162 ARG cc_start: 0.7661 (mtp85) cc_final: 0.7013 (ttm110) REVERT: C 275 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8087 (pp) outliers start: 47 outliers final: 27 residues processed: 207 average time/residue: 0.2715 time to fit residues: 76.7009 Evaluate side-chains 189 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 116 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11279 Z= 0.230 Angle : 0.815 30.584 15292 Z= 0.358 Chirality : 0.045 0.511 1727 Planarity : 0.004 0.041 1919 Dihedral : 8.428 127.287 1604 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.90 % Allowed : 22.59 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.23), residues: 1342 helix: -0.36 (0.22), residues: 580 sheet: -0.87 (0.38), residues: 193 loop : -2.43 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.005 0.001 HIS C 302 PHE 0.022 0.002 PHE A 633 TYR 0.019 0.001 TYR A 311 ARG 0.006 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 172 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6788 (tp30) cc_final: 0.6475 (tp30) REVERT: A 330 LYS cc_start: 0.8112 (tttt) cc_final: 0.7804 (tttm) REVERT: A 367 LYS cc_start: 0.8337 (mttt) cc_final: 0.7983 (mtpt) REVERT: A 519 TYR cc_start: 0.7719 (m-10) cc_final: 0.7435 (m-80) REVERT: A 521 ARG cc_start: 0.6650 (mtt180) cc_final: 0.6175 (mtp85) REVERT: A 628 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7260 (tptt) REVERT: A 941 LEU cc_start: 0.5533 (OUTLIER) cc_final: 0.5285 (tt) REVERT: A 1075 PHE cc_start: 0.7960 (t80) cc_final: 0.7240 (m-80) REVERT: C 275 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8093 (pp) outliers start: 47 outliers final: 36 residues processed: 209 average time/residue: 0.2590 time to fit residues: 74.5040 Evaluate side-chains 204 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 0.0020 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11279 Z= 0.344 Angle : 0.854 32.074 15292 Z= 0.379 Chirality : 0.048 0.553 1727 Planarity : 0.004 0.041 1919 Dihedral : 8.570 133.003 1604 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.90 % Allowed : 21.26 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.22), residues: 1342 helix: -0.48 (0.21), residues: 586 sheet: -1.01 (0.37), residues: 207 loop : -2.42 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 260 HIS 0.004 0.001 HIS A 864 PHE 0.023 0.002 PHE A 971 TYR 0.019 0.002 TYR A 324 ARG 0.003 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 166 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.8338 (pttm) cc_final: 0.8094 (pttp) REVERT: A 330 LYS cc_start: 0.8130 (tttt) cc_final: 0.7827 (tttm) REVERT: A 367 LYS cc_start: 0.8359 (mttt) cc_final: 0.7988 (mtpt) REVERT: A 521 ARG cc_start: 0.6645 (mtt180) cc_final: 0.6163 (mtp85) REVERT: A 613 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7596 (mtm-85) REVERT: A 628 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7272 (tptt) REVERT: A 843 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7630 (ptm-80) REVERT: A 941 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5526 (tt) REVERT: A 1059 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7732 (tp40) REVERT: C 275 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8193 (pp) outliers start: 59 outliers final: 43 residues processed: 214 average time/residue: 0.2517 time to fit residues: 75.7252 Evaluate side-chains 208 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1059 GLN Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 109 optimal weight: 10.0000 chunk 72 optimal weight: 0.0470 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11279 Z= 0.199 Angle : 0.804 30.147 15292 Z= 0.351 Chirality : 0.044 0.471 1727 Planarity : 0.004 0.040 1919 Dihedral : 8.116 131.125 1602 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.99 % Allowed : 22.26 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.23), residues: 1342 helix: -0.23 (0.22), residues: 580 sheet: -0.83 (0.38), residues: 200 loop : -2.28 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.003 0.001 HIS A 114 PHE 0.022 0.001 PHE A 633 TYR 0.015 0.001 TYR A 324 ARG 0.003 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 163 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 162 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8418 (mp) REVERT: A 256 LYS cc_start: 0.8377 (pttm) cc_final: 0.8077 (pttp) REVERT: A 330 LYS cc_start: 0.8110 (tttt) cc_final: 0.7809 (tttm) REVERT: A 367 LYS cc_start: 0.8329 (mttt) cc_final: 0.7978 (mtpt) REVERT: A 519 TYR cc_start: 0.7657 (m-10) cc_final: 0.7402 (m-80) REVERT: A 521 ARG cc_start: 0.6694 (mtt180) cc_final: 0.6186 (mtp85) REVERT: A 613 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7512 (mtm-85) REVERT: A 628 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7188 (tptt) REVERT: A 721 GLU cc_start: 0.4402 (OUTLIER) cc_final: 0.3773 (mp0) REVERT: A 843 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7586 (ptm-80) REVERT: A 941 LEU cc_start: 0.5633 (OUTLIER) cc_final: 0.5357 (tt) REVERT: A 1075 PHE cc_start: 0.7799 (t80) cc_final: 0.7210 (m-80) REVERT: C 155 LYS cc_start: 0.7811 (pttp) cc_final: 0.7591 (pttt) REVERT: C 275 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8146 (pp) REVERT: C 294 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7214 (t0) outliers start: 48 outliers final: 32 residues processed: 202 average time/residue: 0.2593 time to fit residues: 72.6161 Evaluate side-chains 191 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 0.0270 chunk 12 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 0.0270 chunk 112 optimal weight: 0.8980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 828 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11279 Z= 0.155 Angle : 0.789 29.538 15292 Z= 0.338 Chirality : 0.043 0.439 1727 Planarity : 0.004 0.040 1919 Dihedral : 7.570 125.811 1600 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.65 % Allowed : 23.09 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.23), residues: 1342 helix: 0.05 (0.22), residues: 582 sheet: -0.61 (0.39), residues: 198 loop : -2.24 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.002 0.001 HIS A 114 PHE 0.021 0.001 PHE A 633 TYR 0.012 0.001 TYR A 311 ARG 0.008 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 170 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 256 LYS cc_start: 0.8312 (pttm) cc_final: 0.8002 (pttp) REVERT: A 330 LYS cc_start: 0.8106 (tttt) cc_final: 0.7799 (tttm) REVERT: A 367 LYS cc_start: 0.8259 (mttt) cc_final: 0.7960 (mtmt) REVERT: A 378 LYS cc_start: 0.8055 (pttm) cc_final: 0.7842 (pttp) REVERT: A 430 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8141 (tppp) REVERT: A 521 ARG cc_start: 0.6808 (mtt180) cc_final: 0.6320 (mtp85) REVERT: A 628 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7227 (tptt) REVERT: A 639 ASN cc_start: 0.8130 (p0) cc_final: 0.7907 (p0) REVERT: A 721 GLU cc_start: 0.4382 (OUTLIER) cc_final: 0.3787 (mp0) REVERT: A 805 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7016 (pp) REVERT: A 843 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7541 (ptm-80) REVERT: A 941 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.5248 (tt) REVERT: A 1075 PHE cc_start: 0.7778 (t80) cc_final: 0.7161 (m-80) REVERT: C 155 LYS cc_start: 0.7690 (pttp) cc_final: 0.7489 (pttt) REVERT: C 275 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8082 (pp) outliers start: 44 outliers final: 33 residues processed: 204 average time/residue: 0.2572 time to fit residues: 73.3703 Evaluate side-chains 195 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 899 GLN Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 828 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11279 Z= 0.281 Angle : 0.830 31.042 15292 Z= 0.366 Chirality : 0.046 0.494 1727 Planarity : 0.004 0.042 1919 Dihedral : 7.779 130.274 1600 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.82 % Allowed : 22.59 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.23), residues: 1342 helix: -0.12 (0.22), residues: 582 sheet: -0.63 (0.37), residues: 205 loop : -2.25 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 323 HIS 0.004 0.001 HIS A 864 PHE 0.023 0.002 PHE A 633 TYR 0.022 0.002 TYR A 311 ARG 0.006 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 159 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8145 (tttt) cc_final: 0.7831 (tttm) REVERT: A 367 LYS cc_start: 0.8319 (mttt) cc_final: 0.7965 (mtpt) REVERT: A 430 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8117 (tppp) REVERT: A 521 ARG cc_start: 0.6794 (mtt180) cc_final: 0.6288 (mtp85) REVERT: A 628 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7138 (tptt) REVERT: A 805 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7102 (pp) REVERT: A 843 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7614 (ptm-80) REVERT: A 941 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.5371 (tt) REVERT: A 943 MET cc_start: 0.7690 (tpt) cc_final: 0.4704 (tpt) REVERT: A 1075 PHE cc_start: 0.7928 (t80) cc_final: 0.7232 (m-80) REVERT: C 275 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8195 (pp) outliers start: 46 outliers final: 35 residues processed: 196 average time/residue: 0.2504 time to fit residues: 69.2800 Evaluate side-chains 195 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 88 optimal weight: 0.0050 chunk 133 optimal weight: 0.8980 chunk 122 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 82 optimal weight: 0.0980 chunk 65 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 0.0570 overall best weight: 0.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11279 Z= 0.145 Angle : 0.792 29.623 15292 Z= 0.341 Chirality : 0.043 0.422 1727 Planarity : 0.004 0.039 1919 Dihedral : 7.249 123.835 1597 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.74 % Allowed : 23.75 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.23), residues: 1342 helix: 0.17 (0.22), residues: 579 sheet: -0.54 (0.38), residues: 205 loop : -2.12 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 323 HIS 0.002 0.001 HIS A 716 PHE 0.019 0.001 PHE A 633 TYR 0.013 0.001 TYR A 311 ARG 0.006 0.000 ARG C 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8092 (tttt) cc_final: 0.7807 (tttm) REVERT: A 378 LYS cc_start: 0.8034 (pttm) cc_final: 0.7771 (pttp) REVERT: A 521 ARG cc_start: 0.6755 (mtt180) cc_final: 0.6287 (mtp85) REVERT: A 628 LYS cc_start: 0.7704 (ttmt) cc_final: 0.6930 (tptm) REVERT: A 843 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7473 (ptm-80) REVERT: A 941 LEU cc_start: 0.5475 (OUTLIER) cc_final: 0.5256 (tt) REVERT: A 943 MET cc_start: 0.7522 (tpt) cc_final: 0.4641 (tpt) REVERT: A 1075 PHE cc_start: 0.7761 (t80) cc_final: 0.7148 (m-80) REVERT: C 136 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7621 (pttt) REVERT: C 275 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8082 (pp) outliers start: 33 outliers final: 26 residues processed: 198 average time/residue: 0.2471 time to fit residues: 68.2629 Evaluate side-chains 191 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 109 optimal weight: 0.0470 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.173639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.133147 restraints weight = 11210.070| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.62 r_work: 0.3003 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.211 11279 Z= 0.265 Angle : 1.051 59.193 15292 Z= 0.533 Chirality : 0.044 0.423 1727 Planarity : 0.004 0.039 1919 Dihedral : 7.246 123.814 1597 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.49 % Allowed : 24.25 % Favored : 73.26 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1342 helix: 0.18 (0.22), residues: 579 sheet: -0.52 (0.38), residues: 205 loop : -2.11 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 323 HIS 0.002 0.001 HIS A 716 PHE 0.020 0.001 PHE A 633 TYR 0.012 0.001 TYR A 311 ARG 0.006 0.000 ARG C 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2554.64 seconds wall clock time: 48 minutes 30.14 seconds (2910.14 seconds total)