Starting phenix.real_space_refine on Mon Aug 25 10:35:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jj0_36336/08_2025/8jj0_36336.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jj0_36336/08_2025/8jj0_36336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jj0_36336/08_2025/8jj0_36336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jj0_36336/08_2025/8jj0_36336.map" model { file = "/net/cci-nas-00/data/ceres_data/8jj0_36336/08_2025/8jj0_36336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jj0_36336/08_2025/8jj0_36336.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 155 5.16 5 C 17421 2.51 5 N 4548 2.21 5 O 5067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27191 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5876 Classifications: {'peptide': 749} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 29, 'TRANS': 719} Chain breaks: 5 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 6051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6051 Classifications: {'peptide': 773} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 31, 'TRANS': 741} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 5844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5844 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 27, 'TRANS': 715} Chain breaks: 5 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 6052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6052 Classifications: {'peptide': 773} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 31, 'TRANS': 741} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "E" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1617 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Chain breaks: 1 Chain: "F" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1611 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 198} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 7.33, per 1000 atoms: 0.27 Number of scatterers: 27191 At special positions: 0 Unit cell: (165.24, 169.56, 204.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 155 16.00 O 5067 8.00 N 4548 7.00 C 17421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 79 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 900 " - " ASN B 61 " " NAG B 901 " - " ASN B 203 " " NAG B 902 " - " ASN B 471 " " NAG B 903 " - " ASN B 771 " " NAG C 900 " - " ASN C 687 " " NAG D 901 " - " ASN D 276 " " NAG D 902 " - " ASN D 471 " " NAG D 903 " - " ASN D 771 " " NAG G 1 " - " ASN D 61 " Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6476 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 40 sheets defined 40.5% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.895A pdb=" N GLN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.560A pdb=" N THR A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 287 through 310 removed outlier: 3.759A pdb=" N PHE A 310 " --> pdb=" O MET A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 515 through 522 removed outlier: 3.515A pdb=" N VAL A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 579 Processing helix chain 'A' and resid 600 through 611 removed outlier: 3.515A pdb=" N ILE A 605 " --> pdb=" O ILE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 654 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.604A pdb=" N PHE A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 785 through 795 removed outlier: 4.283A pdb=" N GLU A 789 " --> pdb=" O ASP A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 837 removed outlier: 4.013A pdb=" N ALA A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 52 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 103 through 112 removed outlier: 4.581A pdb=" N VAL B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 3.504A pdb=" N TYR B 128 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 159 Processing helix chain 'B' and resid 170 through 188 removed outlier: 4.050A pdb=" N GLU B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 224 through 238 Processing helix chain 'B' and resid 255 through 262 Processing helix chain 'B' and resid 276 through 299 Processing helix chain 'B' and resid 317 through 328 Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.573A pdb=" N TYR B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 583 Processing helix chain 'B' and resid 605 through 615 Processing helix chain 'B' and resid 628 through 657 Processing helix chain 'B' and resid 669 through 674 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 699 through 708 Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.911A pdb=" N PHE B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 782 Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 810 through 843 removed outlier: 3.984A pdb=" N VAL B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU B 834 " --> pdb=" O LEU B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 129 through 133 removed outlier: 4.431A pdb=" N MET C 133 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 180 through 193 Processing helix chain 'C' and resid 213 through 221 removed outlier: 3.780A pdb=" N VAL C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 287 through 308 Processing helix chain 'C' and resid 334 through 339 Processing helix chain 'C' and resid 379 through 383 removed outlier: 3.811A pdb=" N THR C 382 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 472 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'C' and resid 515 through 522 removed outlier: 3.781A pdb=" N GLU C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 579 removed outlier: 3.965A pdb=" N MET C 564 " --> pdb=" O MET C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 611 Processing helix chain 'C' and resid 627 through 654 removed outlier: 4.024A pdb=" N VAL C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.972A pdb=" N GLN C 671 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 676 removed outlier: 3.870A pdb=" N TYR C 676 " --> pdb=" O PRO C 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 673 through 676' Processing helix chain 'C' and resid 688 through 698 Processing helix chain 'C' and resid 698 through 707 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 742 through 746 removed outlier: 4.181A pdb=" N LYS C 746 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 786 through 793 Processing helix chain 'C' and resid 814 through 837 removed outlier: 3.584A pdb=" N ALA C 818 " --> pdb=" O ILE C 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 51 Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.780A pdb=" N SER D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 114 removed outlier: 4.142A pdb=" N TYR D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 130 removed outlier: 3.602A pdb=" N ASP D 130 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 158 Processing helix chain 'D' and resid 170 through 187 removed outlier: 4.061A pdb=" N ARG D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 224 through 238 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 256 through 262 Processing helix chain 'D' and resid 276 through 299 Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 457 through 471 removed outlier: 3.640A pdb=" N ASP D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 494 removed outlier: 3.560A pdb=" N SER D 493 " --> pdb=" O VAL D 490 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN D 494 " --> pdb=" O ASN D 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 490 through 494' Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.835A pdb=" N TYR D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 583 Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 628 through 656 Processing helix chain 'D' and resid 669 through 674 removed outlier: 3.718A pdb=" N ASN D 674 " --> pdb=" O PRO D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 699 through 708 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 732 through 743 Processing helix chain 'D' and resid 768 through 782 Processing helix chain 'D' and resid 782 through 794 removed outlier: 4.167A pdb=" N GLU D 786 " --> pdb=" O ASN D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 843 removed outlier: 3.751A pdb=" N ILE D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.747A pdb=" N ASP E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 196 through 200 removed outlier: 3.866A pdb=" N LEU E 200 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 183 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.435A pdb=" N LEU A 98 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE A 124 " --> pdb=" O PHE A 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 6.589A pdb=" N SER A 171 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 256 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU A 276 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 373 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 409 removed outlier: 3.729A pdb=" N ASP A 523 " --> pdb=" O LEU A 765 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 420 removed outlier: 3.615A pdb=" N VAL A 452 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 434 " --> pdb=" O CYS A 456 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA7, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA8, first strand: chain 'A' and resid 533 through 535 removed outlier: 3.625A pdb=" N SER A 534 " --> pdb=" O TYR A 730 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 27 through 29 removed outlier: 7.085A pdb=" N VAL B 27 " --> pdb=" O ASN B 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 32 through 33 removed outlier: 3.503A pdb=" N LEU B 33 " --> pdb=" O VAL B 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 90 through 91 removed outlier: 6.057A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL B 118 " --> pdb=" O LEU B 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 164 through 167 removed outlier: 6.445A pdb=" N ILE B 164 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N SER B 222 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU B 166 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 267 through 271 removed outlier: 6.956A pdb=" N TYR B 351 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE B 366 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE B 353 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB6, first strand: chain 'B' and resid 514 through 518 removed outlier: 5.679A pdb=" N LEU B 517 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY B 759 " --> pdb=" O LEU B 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 681 through 682 removed outlier: 6.838A pdb=" N ALA B 682 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP B 731 " --> pdb=" O THR B 539 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 540 " --> pdb=" O THR B 749 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.852A pdb=" N LEU C 72 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C 40 " --> pdb=" O LEU C 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 124 through 126 Processing sheet with id=AC1, first strand: chain 'C' and resid 169 through 173 removed outlier: 8.653A pdb=" N PHE C 170 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL C 203 " --> pdb=" O PHE C 170 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU C 172 " --> pdb=" O VAL C 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 226 through 227 removed outlier: 3.549A pdb=" N VAL C 279 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 365 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AC4, first strand: chain 'C' and resid 434 through 438 removed outlier: 3.917A pdb=" N LYS C 438 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL C 452 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 507 through 508 removed outlier: 3.818A pdb=" N ASP C 523 " --> pdb=" O LEU C 765 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 727 through 731 removed outlier: 3.842A pdb=" N TYR C 730 " --> pdb=" O SER C 534 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 61 through 62 removed outlier: 8.205A pdb=" N ASN D 28 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE D 90 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL D 118 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 164 through 167 removed outlier: 5.772A pdb=" N ILE D 164 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N SER D 222 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU D 166 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 267 through 269 removed outlier: 6.415A pdb=" N ASN D 355 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLN D 363 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLN D 357 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 366 " --> pdb=" O ILE D 373 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 330 through 333 removed outlier: 4.301A pdb=" N ASP D 332 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY D 336 " --> pdb=" O ASP D 332 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 476 through 478 removed outlier: 3.614A pdb=" N VAL D 401 " --> pdb=" O MET D 512 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL D 514 " --> pdb=" O VAL D 401 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ALA D 515 " --> pdb=" O GLY D 759 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLY D 759 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 412 through 413 removed outlier: 3.540A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 681 through 682 removed outlier: 6.875A pdb=" N ALA D 682 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 747 " --> pdb=" O VAL D 542 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.618A pdb=" N GLY E 10 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E 120 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 35 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 131 through 134 removed outlier: 3.833A pdb=" N SER E 131 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU E 149 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR E 187 " --> pdb=" O ASP E 155 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL E 192 " --> pdb=" O HIS E 175 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS E 175 " --> pdb=" O VAL E 192 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 163 through 165 removed outlier: 4.016A pdb=" N CYS E 207 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS E 220 " --> pdb=" O CYS E 207 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR E 216 " --> pdb=" O HIS E 211 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AE1, first strand: chain 'F' and resid 11 through 12 removed outlier: 7.213A pdb=" N LEU F 11 " --> pdb=" O ASP F 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.628A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 114 through 118 removed outlier: 4.060A pdb=" N VAL F 133 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA F 130 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU F 181 " --> pdb=" O ALA F 130 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL F 132 " --> pdb=" O LEU F 179 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 153 through 154 removed outlier: 3.500A pdb=" N ALA F 193 " --> pdb=" O LYS F 149 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL F 205 " --> pdb=" O VAL F 196 " (cutoff:3.500A) 1130 hydrogen bonds defined for protein. 3258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8687 1.34 - 1.46: 6599 1.46 - 1.58: 12258 1.58 - 1.70: 0 1.70 - 1.82: 266 Bond restraints: 27810 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.82e+00 bond pdb=" C1 NAG C 900 " pdb=" O5 NAG C 900 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C1 NAG D 903 " pdb=" O5 NAG D 903 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG D 902 " pdb=" O5 NAG D 902 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 NAG B 900 " pdb=" O5 NAG B 900 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 27805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 37298 1.73 - 3.46: 393 3.46 - 5.19: 38 5.19 - 6.92: 7 6.92 - 8.65: 4 Bond angle restraints: 37740 Sorted by residual: angle pdb=" N VAL D 793 " pdb=" CA VAL D 793 " pdb=" C VAL D 793 " ideal model delta sigma weight residual 113.71 110.98 2.73 9.50e-01 1.11e+00 8.23e+00 angle pdb=" N VAL B 793 " pdb=" CA VAL B 793 " pdb=" C VAL B 793 " ideal model delta sigma weight residual 113.47 110.64 2.83 1.01e+00 9.80e-01 7.88e+00 angle pdb=" N ARG A 386 " pdb=" CA ARG A 386 " pdb=" C ARG A 386 " ideal model delta sigma weight residual 114.04 110.64 3.40 1.24e+00 6.50e-01 7.52e+00 angle pdb=" C PRO E 158 " pdb=" N GLU E 159 " pdb=" CA GLU E 159 " ideal model delta sigma weight residual 121.80 128.44 -6.64 2.44e+00 1.68e-01 7.40e+00 angle pdb=" N LYS D 685 " pdb=" CA LYS D 685 " pdb=" C LYS D 685 " ideal model delta sigma weight residual 108.19 111.60 -3.41 1.29e+00 6.01e-01 7.01e+00 ... (remaining 37735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 15713 17.81 - 35.62: 760 35.62 - 53.43: 144 53.43 - 71.25: 16 71.25 - 89.06: 10 Dihedral angle restraints: 16643 sinusoidal: 6614 harmonic: 10029 Sorted by residual: dihedral pdb=" CA ARG B 115 " pdb=" C ARG B 115 " pdb=" N ILE B 116 " pdb=" CA ILE B 116 " ideal model delta harmonic sigma weight residual -180.00 -163.67 -16.33 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU A 412 " pdb=" CG GLU A 412 " pdb=" CD GLU A 412 " pdb=" OE1 GLU A 412 " ideal model delta sinusoidal sigma weight residual 0.00 89.06 -89.06 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU F 187 " pdb=" CG GLU F 187 " pdb=" CD GLU F 187 " pdb=" OE1 GLU F 187 " ideal model delta sinusoidal sigma weight residual 0.00 85.81 -85.81 1 3.00e+01 1.11e-03 9.89e+00 ... (remaining 16640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2943 0.032 - 0.063: 880 0.063 - 0.095: 277 0.095 - 0.126: 196 0.126 - 0.158: 9 Chirality restraints: 4305 Sorted by residual: chirality pdb=" CG LEU D 195 " pdb=" CB LEU D 195 " pdb=" CD1 LEU D 195 " pdb=" CD2 LEU D 195 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CB ILE A 222 " pdb=" CA ILE A 222 " pdb=" CG1 ILE A 222 " pdb=" CG2 ILE A 222 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" C1 NAG D 902 " pdb=" ND2 ASN D 471 " pdb=" C2 NAG D 902 " pdb=" O5 NAG D 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 4302 not shown) Planarity restraints: 4770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 95 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO B 96 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 94 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 95 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 318 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO D 319 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.021 5.00e-02 4.00e+02 ... (remaining 4767 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3147 2.75 - 3.29: 28727 3.29 - 3.83: 47308 3.83 - 4.36: 51783 4.36 - 4.90: 89602 Nonbonded interactions: 220567 Sorted by model distance: nonbonded pdb=" O THR B 396 " pdb=" OG1 THR B 473 " model vdw 2.216 3.040 nonbonded pdb=" O SER B 93 " pdb=" OG1 THR B 122 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR C 531 " pdb=" OD1 ASP C 731 " model vdw 2.227 3.040 nonbonded pdb=" OG SER C 225 " pdb=" O ASP C 252 " model vdw 2.253 3.040 nonbonded pdb=" OG SER E 7 " pdb=" OG SER E 21 " model vdw 2.259 3.040 ... (remaining 220562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 211 or (resid 212 through 213 and \ (name N or name CA or name C or name O or name CB )) or resid 214 through 325 or \ (resid 326 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 7 or (resid 328 and (name N or name CA or name C or name O or name CB )) or resi \ d 329 through 395 or (resid 396 and (name N or name CA or name C or name O or na \ me CB )) or resid 397 through 538 or resid 550 through 579 or resid 599 through \ 837)) selection = (chain 'C' and (resid 34 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 58 or (resid 59 throu \ gh 61 and (name N or name CA or name C or name O or name CB )) or resid 62 throu \ gh 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or r \ esid 96 through 193 or (resid 194 and (name N or name CA or name C or name O or \ name CB )) or resid 195 through 292 or (resid 293 and (name N or name CA or name \ C or name O or name CB )) or resid 294 through 535 or (resid 536 and (name N or \ name CA or name C or name O or name CB )) or resid 537 through 654 or (resid 66 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 661 through \ 665 or (resid 666 and (name N or name CA or name C or name O or name CB )) or re \ sid 667 through 837)) } ncs_group { reference = (chain 'B' and (resid 25 through 294 or (resid 295 and (name N or name CA or nam \ e C or name O or name CB )) or resid 296 through 488 or (resid 489 and (name N o \ r name CA or name C or name O or name CB )) or resid 490 through 577 or (resid 5 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 579 through \ 616 or resid 627 through 902)) selection = (chain 'D' and ((resid 25 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 34 or (resid 35 and (name N or name CA or name C or name \ O or name CB )) or resid 36 through 83 or (resid 84 and (name N or name CA or na \ me C or name O or name CB )) or resid 85 through 326 or (resid 327 and (name N o \ r name CA or name C or name O or name CB )) or resid 328 through 414 or (resid 4 \ 15 and (name N or name CA or name C or name O or name CB )) or resid 416 or (res \ id 417 and (name N or name CA or name C or name O or name CB )) or resid 418 thr \ ough 795 or resid 809 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.400 Find NCS groups from input model: 0.610 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.002 0.039 27834 Z= 0.095 Angle : 0.454 8.650 37798 Z= 0.233 Chirality : 0.040 0.158 4305 Planarity : 0.003 0.050 4761 Dihedral : 10.593 89.057 10125 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.89 % Favored : 93.79 % Rotamer: Outliers : 6.32 % Allowed : 8.53 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.16), residues: 3413 helix: 2.51 (0.15), residues: 1330 sheet: -0.17 (0.28), residues: 433 loop : -0.94 (0.17), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.009 0.001 TYR D 647 PHE 0.009 0.001 PHE D 639 TRP 0.010 0.001 TRP E 110 HIS 0.003 0.000 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00180 (27810) covalent geometry : angle 0.45232 (37740) SS BOND : bond 0.00124 ( 14) SS BOND : angle 0.58597 ( 28) hydrogen bonds : bond 0.15692 ( 1130) hydrogen bonds : angle 6.06171 ( 3258) link_BETA1-4 : bond 0.00934 ( 1) link_BETA1-4 : angle 1.43912 ( 3) link_NAG-ASN : bond 0.00322 ( 9) link_NAG-ASN : angle 1.58639 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 176 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.8762 (mpp) cc_final: 0.7894 (mtt) REVERT: A 425 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8449 (pp) REVERT: A 472 LYS cc_start: 0.9022 (mttt) cc_final: 0.8583 (ptpp) REVERT: A 507 MET cc_start: 0.8271 (ttm) cc_final: 0.8011 (ttm) REVERT: B 125 MET cc_start: 0.9229 (mmm) cc_final: 0.9000 (mtp) REVERT: B 240 MET cc_start: 0.8047 (mmm) cc_final: 0.7651 (mmp) REVERT: B 249 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8641 (t) REVERT: B 379 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8856 (tp) REVERT: B 514 VAL cc_start: 0.9367 (OUTLIER) cc_final: 0.8825 (p) REVERT: C 122 VAL cc_start: 0.3331 (OUTLIER) cc_final: 0.2960 (t) REVERT: C 162 MET cc_start: 0.8671 (mtm) cc_final: 0.8435 (mtp) REVERT: C 198 TRP cc_start: 0.6836 (p90) cc_final: 0.6187 (p90) REVERT: C 199 ASP cc_start: 0.8922 (m-30) cc_final: 0.8627 (p0) REVERT: C 338 MET cc_start: 0.7379 (tpp) cc_final: 0.6917 (tpp) REVERT: C 767 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8279 (tppt) REVERT: C 828 MET cc_start: 0.8063 (mmt) cc_final: 0.7501 (ptm) REVERT: D 125 MET cc_start: 0.7959 (mmm) cc_final: 0.7717 (mmm) REVERT: D 315 TRP cc_start: 0.7534 (OUTLIER) cc_final: 0.6323 (t60) REVERT: D 512 MET cc_start: 0.7881 (tpp) cc_final: 0.7538 (tpp) REVERT: D 695 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8434 (mmp80) REVERT: E 34 MET cc_start: 0.9084 (mmm) cc_final: 0.8591 (mpp) REVERT: E 37 ILE cc_start: 0.9119 (tt) cc_final: 0.7607 (mp) REVERT: E 105 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.6650 (p90) REVERT: E 155 ASP cc_start: 0.8506 (m-30) cc_final: 0.8151 (m-30) REVERT: E 218 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7922 (m) REVERT: F 209 PHE cc_start: 0.4654 (OUTLIER) cc_final: 0.4314 (m-10) outliers start: 186 outliers final: 56 residues processed: 352 average time/residue: 0.2204 time to fit residues: 117.1609 Evaluate side-chains 202 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 135 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN A 816 ASN ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN B 101 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 GLN C 35 ASN C 59 GLN C 332 HIS C 766 GLN D 171 HIS D 491 ASN D 571 HIS D 696 GLN D 705 HIS F 3 GLN F 37 GLN F 55 GLN ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.028052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.021938 restraints weight = 523886.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.022502 restraints weight = 330049.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.022897 restraints weight = 238178.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.023166 restraints weight = 187556.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.023340 restraints weight = 158129.958| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27834 Z= 0.259 Angle : 0.679 9.524 37798 Z= 0.357 Chirality : 0.045 0.330 4305 Planarity : 0.005 0.072 4761 Dihedral : 4.633 45.957 3897 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.97 % Favored : 91.71 % Rotamer: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.15), residues: 3413 helix: 1.89 (0.14), residues: 1329 sheet: -0.93 (0.25), residues: 452 loop : -1.12 (0.17), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 489 TYR 0.029 0.002 TYR D 647 PHE 0.031 0.002 PHE D 609 TRP 0.036 0.002 TRP A 198 HIS 0.008 0.002 HIS D 571 Details of bonding type rmsd covalent geometry : bond 0.00539 (27810) covalent geometry : angle 0.67412 (37740) SS BOND : bond 0.00921 ( 14) SS BOND : angle 1.89748 ( 28) hydrogen bonds : bond 0.03776 ( 1130) hydrogen bonds : angle 5.26909 ( 3258) link_BETA1-4 : bond 0.00222 ( 1) link_BETA1-4 : angle 1.58992 ( 3) link_NAG-ASN : bond 0.01232 ( 9) link_NAG-ASN : angle 2.65886 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8728 (tpp) cc_final: 0.8370 (tpp) REVERT: A 306 MET cc_start: 0.8352 (tpt) cc_final: 0.8118 (tpp) REVERT: A 324 MET cc_start: 0.8724 (mpp) cc_final: 0.7723 (mtt) REVERT: A 472 LYS cc_start: 0.9135 (mttt) cc_final: 0.8733 (ptpp) REVERT: A 507 MET cc_start: 0.8785 (ttm) cc_final: 0.8522 (ttm) REVERT: A 705 MET cc_start: 0.8684 (mmm) cc_final: 0.8340 (mmm) REVERT: A 788 MET cc_start: 0.9351 (mmm) cc_final: 0.9077 (mmm) REVERT: B 125 MET cc_start: 0.9337 (mmm) cc_final: 0.9001 (mtp) REVERT: B 154 MET cc_start: 0.9232 (tmm) cc_final: 0.8596 (tmm) REVERT: B 240 MET cc_start: 0.8096 (mmm) cc_final: 0.7369 (mmm) REVERT: B 706 MET cc_start: 0.9348 (mtm) cc_final: 0.9129 (mtm) REVERT: C 338 MET cc_start: 0.8489 (tpp) cc_final: 0.7697 (tpp) REVERT: C 630 MET cc_start: 0.7282 (tmm) cc_final: 0.6530 (ptm) REVERT: C 828 MET cc_start: 0.7685 (mmt) cc_final: 0.7112 (ppp) REVERT: D 125 MET cc_start: 0.8137 (mmm) cc_final: 0.7885 (mmm) REVERT: D 394 MET cc_start: 0.8106 (mmp) cc_final: 0.7774 (mmp) REVERT: D 512 MET cc_start: 0.8101 (tpp) cc_final: 0.7876 (tpp) REVERT: E 83 MET cc_start: 0.8808 (mpp) cc_final: 0.8548 (mpp) outliers start: 4 outliers final: 0 residues processed: 138 average time/residue: 0.1880 time to fit residues: 42.5227 Evaluate side-chains 121 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 10 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 327 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN C 335 HIS C 671 GLN E 208 ASN F 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.027962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.021845 restraints weight = 520090.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.022410 restraints weight = 327843.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.022795 restraints weight = 236981.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.023070 restraints weight = 187201.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.023243 restraints weight = 158223.622| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27834 Z= 0.180 Angle : 0.577 8.236 37798 Z= 0.303 Chirality : 0.043 0.214 4305 Planarity : 0.004 0.057 4761 Dihedral : 4.503 44.318 3897 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.32 % Favored : 92.35 % Rotamer: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.15), residues: 3413 helix: 1.79 (0.14), residues: 1329 sheet: -1.21 (0.24), residues: 488 loop : -1.23 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 386 TYR 0.026 0.002 TYR D 647 PHE 0.022 0.001 PHE C 613 TRP 0.017 0.001 TRP A 390 HIS 0.010 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00376 (27810) covalent geometry : angle 0.57435 (37740) SS BOND : bond 0.00651 ( 14) SS BOND : angle 1.41115 ( 28) hydrogen bonds : bond 0.03220 ( 1130) hydrogen bonds : angle 4.95801 ( 3258) link_BETA1-4 : bond 0.00142 ( 1) link_BETA1-4 : angle 0.98865 ( 3) link_NAG-ASN : bond 0.00332 ( 9) link_NAG-ASN : angle 1.79686 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8682 (tpp) cc_final: 0.8399 (tpp) REVERT: A 324 MET cc_start: 0.8783 (mpp) cc_final: 0.7750 (mtt) REVERT: A 472 LYS cc_start: 0.9114 (mttt) cc_final: 0.8725 (ptpp) REVERT: A 507 MET cc_start: 0.8673 (ttm) cc_final: 0.8402 (ttm) REVERT: A 705 MET cc_start: 0.8638 (mmm) cc_final: 0.8381 (mmm) REVERT: A 788 MET cc_start: 0.9287 (mmm) cc_final: 0.9014 (mmm) REVERT: B 125 MET cc_start: 0.9271 (mmm) cc_final: 0.8977 (mtp) REVERT: B 240 MET cc_start: 0.8097 (mmm) cc_final: 0.7258 (mmm) REVERT: B 326 MET cc_start: 0.8094 (mpp) cc_final: 0.7773 (ptt) REVERT: B 512 MET cc_start: 0.8462 (mmp) cc_final: 0.8114 (mmp) REVERT: B 762 MET cc_start: 0.7119 (mtp) cc_final: 0.6700 (mtp) REVERT: C 133 MET cc_start: 0.9362 (mpp) cc_final: 0.9160 (mpp) REVERT: C 158 MET cc_start: 0.8767 (mtm) cc_final: 0.8523 (mtm) REVERT: C 198 TRP cc_start: 0.6581 (p90) cc_final: 0.6147 (p90) REVERT: C 338 MET cc_start: 0.8395 (tpp) cc_final: 0.7563 (tpp) REVERT: C 450 MET cc_start: 0.9107 (pmm) cc_final: 0.8887 (pmm) REVERT: C 828 MET cc_start: 0.7642 (mmt) cc_final: 0.7086 (ppp) REVERT: D 125 MET cc_start: 0.7926 (mmm) cc_final: 0.7638 (mmm) REVERT: D 394 MET cc_start: 0.8173 (mmp) cc_final: 0.7787 (mmp) REVERT: D 501 MET cc_start: 0.9032 (mmp) cc_final: 0.8386 (mmp) REVERT: D 512 MET cc_start: 0.7898 (tpp) cc_final: 0.7659 (tpp) REVERT: D 706 MET cc_start: 0.9258 (mtp) cc_final: 0.8998 (mtp) REVERT: E 83 MET cc_start: 0.8716 (mpp) cc_final: 0.8395 (mpp) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.1747 time to fit residues: 38.0370 Evaluate side-chains 124 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 242 optimal weight: 4.9990 chunk 329 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 320 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN E 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.027440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.021648 restraints weight = 523891.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.022172 restraints weight = 332777.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.022549 restraints weight = 241070.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.022793 restraints weight = 189960.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.022943 restraints weight = 161201.862| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27834 Z= 0.202 Angle : 0.613 11.131 37798 Z= 0.320 Chirality : 0.043 0.199 4305 Planarity : 0.004 0.083 4761 Dihedral : 4.687 45.831 3897 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.58 % Favored : 91.06 % Rotamer: Outliers : 0.07 % Allowed : 3.98 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.15), residues: 3413 helix: 1.58 (0.14), residues: 1334 sheet: -1.39 (0.23), residues: 491 loop : -1.35 (0.17), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 694 TYR 0.029 0.002 TYR D 647 PHE 0.026 0.002 PHE D 639 TRP 0.018 0.002 TRP A 390 HIS 0.007 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00425 (27810) covalent geometry : angle 0.61007 (37740) SS BOND : bond 0.00288 ( 14) SS BOND : angle 1.49551 ( 28) hydrogen bonds : bond 0.03207 ( 1130) hydrogen bonds : angle 4.98963 ( 3258) link_BETA1-4 : bond 0.00140 ( 1) link_BETA1-4 : angle 1.77621 ( 3) link_NAG-ASN : bond 0.00221 ( 9) link_NAG-ASN : angle 1.77256 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8656 (tpp) cc_final: 0.8407 (tpp) REVERT: A 324 MET cc_start: 0.8877 (mpp) cc_final: 0.8057 (mtt) REVERT: A 472 LYS cc_start: 0.9210 (mttt) cc_final: 0.8882 (ptpp) REVERT: A 705 MET cc_start: 0.8720 (mmm) cc_final: 0.8397 (mmm) REVERT: A 788 MET cc_start: 0.9352 (mmm) cc_final: 0.9056 (mmm) REVERT: B 125 MET cc_start: 0.9374 (mmm) cc_final: 0.9019 (mtp) REVERT: B 209 MET cc_start: 0.8939 (mmm) cc_final: 0.8698 (mmm) REVERT: B 240 MET cc_start: 0.8282 (mmm) cc_final: 0.7573 (mmm) REVERT: B 326 MET cc_start: 0.8159 (mpp) cc_final: 0.7892 (ptt) REVERT: B 512 MET cc_start: 0.8474 (mmp) cc_final: 0.8059 (mmp) REVERT: B 762 MET cc_start: 0.7319 (mtp) cc_final: 0.6862 (mtp) REVERT: C 133 MET cc_start: 0.9311 (mpp) cc_final: 0.8963 (mpp) REVERT: C 158 MET cc_start: 0.8864 (mtm) cc_final: 0.8589 (mtm) REVERT: C 338 MET cc_start: 0.8523 (tpp) cc_final: 0.7627 (tpp) REVERT: C 507 MET cc_start: 0.7844 (mmp) cc_final: 0.7466 (mmm) REVERT: C 630 MET cc_start: 0.7444 (tmm) cc_final: 0.6581 (ptm) REVERT: C 828 MET cc_start: 0.7702 (mmt) cc_final: 0.7102 (ppp) REVERT: D 125 MET cc_start: 0.8239 (mmm) cc_final: 0.7904 (mmm) REVERT: D 394 MET cc_start: 0.8268 (mmp) cc_final: 0.7899 (mmp) REVERT: D 501 MET cc_start: 0.9085 (mmp) cc_final: 0.8507 (mmp) REVERT: D 512 MET cc_start: 0.8048 (tpp) cc_final: 0.7733 (tpp) REVERT: E 83 MET cc_start: 0.8695 (mpp) cc_final: 0.8379 (mpp) outliers start: 2 outliers final: 0 residues processed: 130 average time/residue: 0.1722 time to fit residues: 37.8542 Evaluate side-chains 121 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 292 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 280 optimal weight: 30.0000 chunk 99 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 133 optimal weight: 0.1980 chunk 331 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.027787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.022015 restraints weight = 513824.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.022532 restraints weight = 330249.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.022883 restraints weight = 241745.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.023133 restraints weight = 192464.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.023288 restraints weight = 163341.667| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27834 Z= 0.124 Angle : 0.564 8.245 37798 Z= 0.291 Chirality : 0.042 0.193 4305 Planarity : 0.004 0.067 4761 Dihedral : 4.450 46.126 3897 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.47 % Favored : 92.15 % Rotamer: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.15), residues: 3413 helix: 1.64 (0.14), residues: 1333 sheet: -1.42 (0.23), residues: 494 loop : -1.31 (0.17), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 377 TYR 0.028 0.001 TYR D 647 PHE 0.024 0.001 PHE D 639 TRP 0.013 0.001 TRP A 390 HIS 0.010 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00268 (27810) covalent geometry : angle 0.56137 (37740) SS BOND : bond 0.00473 ( 14) SS BOND : angle 1.44047 ( 28) hydrogen bonds : bond 0.02890 ( 1130) hydrogen bonds : angle 4.78594 ( 3258) link_BETA1-4 : bond 0.00874 ( 1) link_BETA1-4 : angle 1.54708 ( 3) link_NAG-ASN : bond 0.00250 ( 9) link_NAG-ASN : angle 1.74663 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8890 (mpp) cc_final: 0.8617 (mpp) REVERT: A 324 MET cc_start: 0.8779 (mpp) cc_final: 0.7644 (mtt) REVERT: A 472 LYS cc_start: 0.9184 (mttt) cc_final: 0.8731 (ptpp) REVERT: A 705 MET cc_start: 0.8647 (mmm) cc_final: 0.8339 (mmm) REVERT: A 788 MET cc_start: 0.9324 (mmm) cc_final: 0.9058 (mmm) REVERT: B 125 MET cc_start: 0.9277 (mmm) cc_final: 0.9027 (mtp) REVERT: B 209 MET cc_start: 0.9045 (mmm) cc_final: 0.8798 (mmm) REVERT: B 240 MET cc_start: 0.8465 (mmm) cc_final: 0.7853 (mmm) REVERT: B 512 MET cc_start: 0.8576 (mmp) cc_final: 0.8143 (mmp) REVERT: B 762 MET cc_start: 0.7330 (mtp) cc_final: 0.7019 (mtp) REVERT: C 133 MET cc_start: 0.9318 (mpp) cc_final: 0.8983 (mpp) REVERT: C 338 MET cc_start: 0.8534 (tpp) cc_final: 0.7671 (tpp) REVERT: C 630 MET cc_start: 0.7523 (tmm) cc_final: 0.6588 (ptm) REVERT: C 828 MET cc_start: 0.7627 (mmt) cc_final: 0.7099 (ppp) REVERT: D 125 MET cc_start: 0.8214 (mmm) cc_final: 0.7866 (mmm) REVERT: D 394 MET cc_start: 0.8186 (mmp) cc_final: 0.7782 (mmp) REVERT: D 501 MET cc_start: 0.9040 (mmp) cc_final: 0.8462 (mmp) REVERT: D 512 MET cc_start: 0.8041 (tpp) cc_final: 0.7705 (tpp) REVERT: E 83 MET cc_start: 0.8617 (mpp) cc_final: 0.8284 (mpp) outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.1725 time to fit residues: 37.3462 Evaluate side-chains 124 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 286 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 333 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 256 optimal weight: 5.9990 chunk 41 optimal weight: 0.0770 chunk 79 optimal weight: 7.9990 chunk 292 optimal weight: 5.9990 chunk 340 optimal weight: 30.0000 chunk 60 optimal weight: 0.9980 overall best weight: 2.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.027672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.021876 restraints weight = 518683.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.022408 restraints weight = 328600.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.022782 restraints weight = 238347.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.023025 restraints weight = 187460.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.023204 restraints weight = 158277.318| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27834 Z= 0.141 Angle : 0.567 11.475 37798 Z= 0.294 Chirality : 0.043 0.196 4305 Planarity : 0.004 0.062 4761 Dihedral : 4.394 45.900 3897 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.06 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.15), residues: 3413 helix: 1.63 (0.14), residues: 1332 sheet: -1.42 (0.23), residues: 490 loop : -1.31 (0.17), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 392 TYR 0.029 0.001 TYR D 647 PHE 0.020 0.001 PHE A 253 TRP 0.012 0.001 TRP A 390 HIS 0.004 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00306 (27810) covalent geometry : angle 0.56390 (37740) SS BOND : bond 0.00482 ( 14) SS BOND : angle 1.44436 ( 28) hydrogen bonds : bond 0.02925 ( 1130) hydrogen bonds : angle 4.76061 ( 3258) link_BETA1-4 : bond 0.00621 ( 1) link_BETA1-4 : angle 1.47866 ( 3) link_NAG-ASN : bond 0.00221 ( 9) link_NAG-ASN : angle 1.73009 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8921 (pmm) cc_final: 0.8714 (pmm) REVERT: A 324 MET cc_start: 0.8783 (mpp) cc_final: 0.7657 (mtt) REVERT: A 472 LYS cc_start: 0.9193 (mttt) cc_final: 0.8761 (ptpp) REVERT: A 507 MET cc_start: 0.8729 (ttm) cc_final: 0.8463 (ttm) REVERT: A 705 MET cc_start: 0.8638 (mmm) cc_final: 0.8333 (mmm) REVERT: A 788 MET cc_start: 0.9281 (mmm) cc_final: 0.9022 (mmm) REVERT: B 125 MET cc_start: 0.9259 (mmm) cc_final: 0.9024 (mtp) REVERT: B 209 MET cc_start: 0.9106 (mmm) cc_final: 0.8900 (mmm) REVERT: B 240 MET cc_start: 0.8519 (mmm) cc_final: 0.7943 (mmm) REVERT: B 512 MET cc_start: 0.8544 (mmp) cc_final: 0.7231 (mmp) REVERT: B 762 MET cc_start: 0.7344 (mtp) cc_final: 0.6755 (mtp) REVERT: C 133 MET cc_start: 0.9329 (mpp) cc_final: 0.8985 (mpp) REVERT: C 162 MET cc_start: 0.8577 (mmm) cc_final: 0.8342 (mmm) REVERT: C 338 MET cc_start: 0.8505 (tpp) cc_final: 0.7670 (tpp) REVERT: D 41 MET cc_start: 0.9213 (tpp) cc_final: 0.8981 (tpt) REVERT: D 125 MET cc_start: 0.8103 (mmm) cc_final: 0.7834 (mmm) REVERT: D 394 MET cc_start: 0.8137 (mmp) cc_final: 0.7716 (mmp) REVERT: D 502 MET cc_start: 0.8425 (mmt) cc_final: 0.7981 (mmt) REVERT: D 512 MET cc_start: 0.7978 (tpp) cc_final: 0.7649 (tpp) REVERT: E 83 MET cc_start: 0.8591 (mpp) cc_final: 0.8259 (mpp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1657 time to fit residues: 35.5901 Evaluate side-chains 121 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 113 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 281 optimal weight: 7.9990 chunk 290 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 251 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN D 293 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.027654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.021594 restraints weight = 514010.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.022156 restraints weight = 321976.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.022553 restraints weight = 230709.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.022813 restraints weight = 181228.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.023009 restraints weight = 152775.272| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27834 Z= 0.159 Angle : 0.590 10.021 37798 Z= 0.305 Chirality : 0.043 0.297 4305 Planarity : 0.004 0.062 4761 Dihedral : 4.484 42.266 3897 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.56 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 3413 helix: 1.56 (0.14), residues: 1330 sheet: -1.51 (0.23), residues: 497 loop : -1.35 (0.17), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 504 TYR 0.028 0.001 TYR D 647 PHE 0.023 0.001 PHE B 321 TRP 0.013 0.001 TRP A 390 HIS 0.010 0.001 HIS C 702 Details of bonding type rmsd covalent geometry : bond 0.00342 (27810) covalent geometry : angle 0.58708 (37740) SS BOND : bond 0.00377 ( 14) SS BOND : angle 1.61102 ( 28) hydrogen bonds : bond 0.03017 ( 1130) hydrogen bonds : angle 4.81012 ( 3258) link_BETA1-4 : bond 0.00080 ( 1) link_BETA1-4 : angle 1.59426 ( 3) link_NAG-ASN : bond 0.00357 ( 9) link_NAG-ASN : angle 1.74010 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8858 (mpp) cc_final: 0.8611 (mpp) REVERT: A 133 MET cc_start: 0.8952 (pmm) cc_final: 0.8690 (pmm) REVERT: A 324 MET cc_start: 0.8823 (mpp) cc_final: 0.7705 (mtt) REVERT: A 472 LYS cc_start: 0.9276 (mttt) cc_final: 0.8873 (ptpp) REVERT: A 701 MET cc_start: 0.9267 (tpt) cc_final: 0.8978 (mmm) REVERT: A 705 MET cc_start: 0.8785 (mmm) cc_final: 0.8461 (mmt) REVERT: A 788 MET cc_start: 0.9411 (mmm) cc_final: 0.9118 (mmm) REVERT: B 125 MET cc_start: 0.9356 (mmm) cc_final: 0.9070 (mtp) REVERT: B 240 MET cc_start: 0.8569 (mmm) cc_final: 0.7927 (mmm) REVERT: B 512 MET cc_start: 0.8584 (mmp) cc_final: 0.7286 (mmp) REVERT: B 762 MET cc_start: 0.7475 (mtp) cc_final: 0.6815 (mtp) REVERT: C 133 MET cc_start: 0.9280 (mpp) cc_final: 0.8896 (mpp) REVERT: C 162 MET cc_start: 0.8635 (mmm) cc_final: 0.8402 (mmm) REVERT: C 200 MET cc_start: 0.9140 (tmm) cc_final: 0.8331 (tmm) REVERT: C 338 MET cc_start: 0.8552 (tpp) cc_final: 0.7658 (tpp) REVERT: C 630 MET cc_start: 0.7457 (tmm) cc_final: 0.6489 (ptm) REVERT: D 41 MET cc_start: 0.9221 (tpp) cc_final: 0.8999 (tpt) REVERT: D 125 MET cc_start: 0.8254 (mmm) cc_final: 0.7943 (mmm) REVERT: D 326 MET cc_start: 0.9408 (mmm) cc_final: 0.8621 (mmm) REVERT: D 394 MET cc_start: 0.8296 (mmp) cc_final: 0.7825 (mmp) REVERT: D 501 MET cc_start: 0.9017 (mmp) cc_final: 0.8398 (mmp) REVERT: D 502 MET cc_start: 0.8577 (mmt) cc_final: 0.8333 (mmt) REVERT: D 512 MET cc_start: 0.8037 (tpp) cc_final: 0.7624 (tpp) REVERT: E 83 MET cc_start: 0.8592 (mpp) cc_final: 0.8213 (mpp) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1441 time to fit residues: 30.2518 Evaluate side-chains 120 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 200 optimal weight: 0.9980 chunk 308 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 277 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 229 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.027710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.021622 restraints weight = 514199.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.022187 restraints weight = 321959.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.022556 restraints weight = 232219.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.022834 restraints weight = 184343.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.023014 restraints weight = 155104.994| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27834 Z= 0.140 Angle : 0.582 9.464 37798 Z= 0.300 Chirality : 0.043 0.239 4305 Planarity : 0.004 0.059 4761 Dihedral : 4.443 40.731 3897 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.38 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.15), residues: 3413 helix: 1.55 (0.14), residues: 1327 sheet: -1.52 (0.23), residues: 497 loop : -1.35 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 681 TYR 0.028 0.001 TYR D 647 PHE 0.022 0.001 PHE A 253 TRP 0.014 0.001 TRP A 390 HIS 0.006 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00301 (27810) covalent geometry : angle 0.57859 (37740) SS BOND : bond 0.00282 ( 14) SS BOND : angle 1.44791 ( 28) hydrogen bonds : bond 0.02927 ( 1130) hydrogen bonds : angle 4.75775 ( 3258) link_BETA1-4 : bond 0.00990 ( 1) link_BETA1-4 : angle 1.68388 ( 3) link_NAG-ASN : bond 0.00285 ( 9) link_NAG-ASN : angle 1.74646 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8883 (mpp) cc_final: 0.8617 (mpp) REVERT: A 133 MET cc_start: 0.8887 (pmm) cc_final: 0.8610 (pmm) REVERT: A 324 MET cc_start: 0.8781 (mpp) cc_final: 0.7615 (mtt) REVERT: A 472 LYS cc_start: 0.9251 (mttt) cc_final: 0.8846 (ptpp) REVERT: A 705 MET cc_start: 0.8791 (mmm) cc_final: 0.8521 (mmp) REVERT: A 788 MET cc_start: 0.9423 (mmm) cc_final: 0.9050 (mmm) REVERT: B 41 MET cc_start: 0.9125 (ptt) cc_final: 0.8883 (ppp) REVERT: B 240 MET cc_start: 0.8625 (mmm) cc_final: 0.8029 (mmm) REVERT: B 512 MET cc_start: 0.8527 (mmp) cc_final: 0.7235 (mmp) REVERT: B 762 MET cc_start: 0.7399 (mtp) cc_final: 0.6786 (mtp) REVERT: C 133 MET cc_start: 0.9275 (mpp) cc_final: 0.8875 (mpp) REVERT: C 162 MET cc_start: 0.8614 (mmm) cc_final: 0.8353 (mmm) REVERT: C 200 MET cc_start: 0.9136 (tmm) cc_final: 0.8400 (tmm) REVERT: C 338 MET cc_start: 0.8565 (tpp) cc_final: 0.7698 (tpp) REVERT: C 630 MET cc_start: 0.7481 (tmm) cc_final: 0.6542 (ptm) REVERT: C 788 MET cc_start: 0.8937 (mmm) cc_final: 0.8371 (mmm) REVERT: D 41 MET cc_start: 0.9233 (tpp) cc_final: 0.9027 (tpt) REVERT: D 125 MET cc_start: 0.8264 (mmm) cc_final: 0.7960 (mmm) REVERT: D 326 MET cc_start: 0.9366 (mmm) cc_final: 0.8635 (mmm) REVERT: D 354 MET cc_start: 0.8838 (mmp) cc_final: 0.7059 (mmp) REVERT: D 394 MET cc_start: 0.8297 (mmp) cc_final: 0.7834 (mmp) REVERT: D 501 MET cc_start: 0.8989 (mmp) cc_final: 0.8413 (mmp) REVERT: D 502 MET cc_start: 0.8510 (mmt) cc_final: 0.8291 (mmt) REVERT: D 512 MET cc_start: 0.8035 (tpp) cc_final: 0.7620 (tpp) REVERT: E 83 MET cc_start: 0.8580 (mpp) cc_final: 0.8197 (mpp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1498 time to fit residues: 31.9739 Evaluate side-chains 121 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 54 optimal weight: 5.9990 chunk 339 optimal weight: 8.9990 chunk 337 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 239 optimal weight: 0.9980 chunk 288 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 340 optimal weight: 30.0000 chunk 312 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 HIS D 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.027346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.021338 restraints weight = 515566.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.021887 restraints weight = 326498.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.022231 restraints weight = 236422.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.022503 restraints weight = 189611.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.022697 restraints weight = 159665.999| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27834 Z= 0.188 Angle : 0.630 8.967 37798 Z= 0.327 Chirality : 0.044 0.198 4305 Planarity : 0.004 0.064 4761 Dihedral : 4.704 42.066 3897 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.00 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.15), residues: 3413 helix: 1.33 (0.14), residues: 1331 sheet: -1.82 (0.22), residues: 527 loop : -1.39 (0.17), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 392 TYR 0.030 0.002 TYR E 105 PHE 0.025 0.002 PHE A 253 TRP 0.015 0.002 TRP C 55 HIS 0.006 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00398 (27810) covalent geometry : angle 0.62652 (37740) SS BOND : bond 0.00614 ( 14) SS BOND : angle 1.66815 ( 28) hydrogen bonds : bond 0.03217 ( 1130) hydrogen bonds : angle 4.88765 ( 3258) link_BETA1-4 : bond 0.00263 ( 1) link_BETA1-4 : angle 1.56144 ( 3) link_NAG-ASN : bond 0.00206 ( 9) link_NAG-ASN : angle 1.76938 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8869 (mpp) cc_final: 0.8592 (mpp) REVERT: A 306 MET cc_start: 0.7794 (tpp) cc_final: 0.7098 (tpp) REVERT: A 324 MET cc_start: 0.8739 (mpp) cc_final: 0.7932 (mtt) REVERT: A 472 LYS cc_start: 0.9251 (mttt) cc_final: 0.8893 (ptpp) REVERT: A 705 MET cc_start: 0.8762 (mmm) cc_final: 0.8525 (mmp) REVERT: B 125 MET cc_start: 0.9505 (mtp) cc_final: 0.9001 (mtp) REVERT: B 240 MET cc_start: 0.8642 (mmm) cc_final: 0.8029 (mmm) REVERT: B 512 MET cc_start: 0.8434 (mmp) cc_final: 0.7130 (mmp) REVERT: B 706 MET cc_start: 0.9285 (mtm) cc_final: 0.9044 (mtm) REVERT: B 762 MET cc_start: 0.7493 (mtp) cc_final: 0.6769 (mtp) REVERT: C 133 MET cc_start: 0.9275 (mpp) cc_final: 0.8890 (mpp) REVERT: C 158 MET cc_start: 0.8795 (mtm) cc_final: 0.8433 (mtm) REVERT: C 162 MET cc_start: 0.8605 (mmm) cc_final: 0.8385 (mmm) REVERT: C 200 MET cc_start: 0.9183 (tmm) cc_final: 0.8467 (tmm) REVERT: C 338 MET cc_start: 0.8443 (tpp) cc_final: 0.7575 (tpp) REVERT: C 630 MET cc_start: 0.7449 (tmm) cc_final: 0.6535 (ptm) REVERT: D 125 MET cc_start: 0.8163 (mmm) cc_final: 0.7887 (mmm) REVERT: D 326 MET cc_start: 0.9342 (mmm) cc_final: 0.8638 (mmm) REVERT: D 394 MET cc_start: 0.8234 (mmp) cc_final: 0.7647 (mmp) REVERT: D 501 MET cc_start: 0.8988 (mmp) cc_final: 0.8441 (mmp) REVERT: D 502 MET cc_start: 0.8487 (mmt) cc_final: 0.8280 (mmt) REVERT: D 512 MET cc_start: 0.8046 (tpp) cc_final: 0.7612 (tpp) REVERT: D 634 MET cc_start: 0.9403 (tpp) cc_final: 0.9027 (mmp) REVERT: E 83 MET cc_start: 0.8593 (mpp) cc_final: 0.8217 (mpp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1450 time to fit residues: 30.3010 Evaluate side-chains 118 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 312 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 chunk 224 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 314 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.027488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.021470 restraints weight = 515823.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.022026 restraints weight = 323524.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.022393 restraints weight = 233277.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.022663 restraints weight = 185307.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.022853 restraints weight = 156051.899| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27834 Z= 0.150 Angle : 0.601 8.875 37798 Z= 0.311 Chirality : 0.044 0.190 4305 Planarity : 0.004 0.062 4761 Dihedral : 4.632 42.053 3897 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.44 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.15), residues: 3413 helix: 1.38 (0.14), residues: 1330 sheet: -1.71 (0.23), residues: 500 loop : -1.40 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 392 TYR 0.030 0.001 TYR E 105 PHE 0.025 0.001 PHE A 253 TRP 0.014 0.001 TRP A 390 HIS 0.004 0.001 HIS C 96 Details of bonding type rmsd covalent geometry : bond 0.00322 (27810) covalent geometry : angle 0.59809 (37740) SS BOND : bond 0.00414 ( 14) SS BOND : angle 1.62600 ( 28) hydrogen bonds : bond 0.03037 ( 1130) hydrogen bonds : angle 4.81503 ( 3258) link_BETA1-4 : bond 0.00742 ( 1) link_BETA1-4 : angle 1.95410 ( 3) link_NAG-ASN : bond 0.00239 ( 9) link_NAG-ASN : angle 1.81441 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8890 (mpp) cc_final: 0.8604 (mpp) REVERT: A 331 MET cc_start: 0.2839 (tpt) cc_final: 0.2519 (tpt) REVERT: A 472 LYS cc_start: 0.9260 (mttt) cc_final: 0.8895 (ptpp) REVERT: A 701 MET cc_start: 0.9088 (tpt) cc_final: 0.8589 (mmm) REVERT: A 705 MET cc_start: 0.8726 (mmm) cc_final: 0.8377 (mmt) REVERT: B 125 MET cc_start: 0.9484 (mtp) cc_final: 0.8961 (mtp) REVERT: B 240 MET cc_start: 0.8639 (mmm) cc_final: 0.7942 (mmm) REVERT: B 326 MET cc_start: 0.8246 (ppp) cc_final: 0.7837 (ppp) REVERT: B 512 MET cc_start: 0.8328 (mmp) cc_final: 0.7070 (mmp) REVERT: B 762 MET cc_start: 0.7731 (mtp) cc_final: 0.7200 (mtp) REVERT: C 133 MET cc_start: 0.9305 (mpp) cc_final: 0.8872 (mpp) REVERT: C 158 MET cc_start: 0.8818 (mtm) cc_final: 0.8431 (mtm) REVERT: C 200 MET cc_start: 0.9172 (tmm) cc_final: 0.8565 (tmm) REVERT: C 338 MET cc_start: 0.8430 (tpp) cc_final: 0.7620 (tpp) REVERT: C 630 MET cc_start: 0.7471 (tmm) cc_final: 0.6563 (ptm) REVERT: C 788 MET cc_start: 0.9001 (mmm) cc_final: 0.8556 (mmm) REVERT: C 828 MET cc_start: 0.7585 (mmt) cc_final: 0.7130 (ptp) REVERT: D 125 MET cc_start: 0.8184 (mmm) cc_final: 0.7919 (mmm) REVERT: D 326 MET cc_start: 0.9387 (mmm) cc_final: 0.8679 (mmm) REVERT: D 354 MET cc_start: 0.8961 (mmp) cc_final: 0.7337 (mmp) REVERT: D 394 MET cc_start: 0.8257 (mmp) cc_final: 0.7710 (mmp) REVERT: D 501 MET cc_start: 0.8928 (mmp) cc_final: 0.8441 (mmp) REVERT: D 512 MET cc_start: 0.8076 (tpp) cc_final: 0.7745 (tpp) REVERT: E 34 MET cc_start: 0.8843 (mmm) cc_final: 0.8523 (mmm) REVERT: E 83 MET cc_start: 0.8578 (mpp) cc_final: 0.8151 (mpp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1410 time to fit residues: 29.4377 Evaluate side-chains 119 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 68 optimal weight: 3.9990 chunk 279 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 338 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 90 optimal weight: 0.1980 chunk 186 optimal weight: 8.9990 chunk 295 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 272 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS B 363 GLN B 705 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.027790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.021707 restraints weight = 509734.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.022273 restraints weight = 318427.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.022686 restraints weight = 227626.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.022940 restraints weight = 178108.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.023138 restraints weight = 150638.520| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27834 Z= 0.116 Angle : 0.590 8.991 37798 Z= 0.303 Chirality : 0.043 0.204 4305 Planarity : 0.004 0.058 4761 Dihedral : 4.487 40.735 3897 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.32 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.15), residues: 3413 helix: 1.46 (0.14), residues: 1328 sheet: -1.59 (0.23), residues: 486 loop : -1.38 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 681 TYR 0.040 0.001 TYR E 105 PHE 0.023 0.001 PHE A 253 TRP 0.011 0.001 TRP E 110 HIS 0.006 0.001 HIS C 168 Details of bonding type rmsd covalent geometry : bond 0.00254 (27810) covalent geometry : angle 0.58657 (37740) SS BOND : bond 0.00403 ( 14) SS BOND : angle 1.54190 ( 28) hydrogen bonds : bond 0.02884 ( 1130) hydrogen bonds : angle 4.68842 ( 3258) link_BETA1-4 : bond 0.00931 ( 1) link_BETA1-4 : angle 1.99320 ( 3) link_NAG-ASN : bond 0.00281 ( 9) link_NAG-ASN : angle 1.76602 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3992.02 seconds wall clock time: 70 minutes 40.73 seconds (4240.73 seconds total)