Starting phenix.real_space_refine on Sun May 25 21:28:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jj0_36336/05_2025/8jj0_36336.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jj0_36336/05_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_36336/05_2025/8jj0_36336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jj0_36336/05_2025/8jj0_36336.map" model { file = "/net/cci-nas-00/data/ceres_data/8jj0_36336/05_2025/8jj0_36336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jj0_36336/05_2025/8jj0_36336.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG: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: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 2} 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: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4, 'PHE:plan': 2, 'ASP:plan': 1} 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: 16.50, per 1000 atoms: 0.61 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: 6.87 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 3.30 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: 9.86 Time building geometry restraints manager: 8.09 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 844 or resid 900 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 844 or resid 901 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: 5.640 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: 0.040 Extract box with map and model: 1.490 Check model and map are aligned: 0.290 Set scattering table: 0.330 Process input model: 60.670 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.860 ------------------------------------------------------------------------------- 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 : 10.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (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 TRP 0.010 0.001 TRP E 110 HIS 0.003 0.000 HIS C 42 PHE 0.009 0.001 PHE D 639 TYR 0.009 0.001 TYR D 647 ARG 0.004 0.000 ARG C 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 9) link_NAG-ASN : angle 1.58639 ( 27) link_BETA1-4 : bond 0.00934 ( 1) link_BETA1-4 : angle 1.43912 ( 3) hydrogen bonds : bond 0.15692 ( 1130) hydrogen bonds : angle 6.06171 ( 3258) SS BOND : bond 0.00124 ( 14) SS BOND : angle 0.58597 ( 28) covalent geometry : bond 0.00180 (27810) covalent geometry : angle 0.45232 (37740) *********************** 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 : 3.007 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: 0.4491 time to fit residues: 239.5746 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 : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 312 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN A 703 GLN ** 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 D 171 HIS D 491 ASN D 571 HIS 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.028859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.022727 restraints weight = 516068.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.023308 restraints weight = 323273.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.023729 restraints weight = 231147.085| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27834 Z= 0.175 Angle : 0.604 9.456 37798 Z= 0.315 Chirality : 0.044 0.248 4305 Planarity : 0.004 0.078 4761 Dihedral : 4.280 44.574 3897 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.15 % Favored : 92.50 % Rotamer: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3413 helix: 2.10 (0.14), residues: 1327 sheet: -0.71 (0.26), residues: 445 loop : -1.06 (0.17), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 315 HIS 0.010 0.001 HIS D 571 PHE 0.028 0.002 PHE D 609 TYR 0.029 0.002 TYR D 647 ARG 0.007 0.001 ARG B 755 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 9) link_NAG-ASN : angle 2.97188 ( 27) link_BETA1-4 : bond 0.00181 ( 1) link_BETA1-4 : angle 1.23080 ( 3) hydrogen bonds : bond 0.03449 ( 1130) hydrogen bonds : angle 5.12440 ( 3258) SS BOND : bond 0.00503 ( 14) SS BOND : angle 2.02182 ( 28) covalent geometry : bond 0.00378 (27810) covalent geometry : angle 0.59696 (37740) *********************** 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 142 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 2.994 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: A 306 MET cc_start: 0.8455 (tpt) cc_final: 0.8235 (tpp) REVERT: A 324 MET cc_start: 0.8750 (mpp) cc_final: 0.7784 (mtt) REVERT: A 472 LYS cc_start: 0.9109 (mttt) cc_final: 0.8657 (ptpp) REVERT: A 507 MET cc_start: 0.8777 (ttm) cc_final: 0.8547 (ttm) REVERT: A 705 MET cc_start: 0.8634 (mmm) cc_final: 0.8398 (mmm) REVERT: A 788 MET cc_start: 0.9279 (mmm) cc_final: 0.8964 (mmm) REVERT: B 125 MET cc_start: 0.9350 (mmm) cc_final: 0.9047 (mtp) REVERT: B 154 MET cc_start: 0.9247 (tmm) cc_final: 0.8776 (tmm) REVERT: B 706 MET cc_start: 0.9365 (mtm) cc_final: 0.9121 (mtm) REVERT: C 338 MET cc_start: 0.8399 (tpp) cc_final: 0.7642 (tpp) REVERT: C 507 MET cc_start: 0.8427 (tpp) cc_final: 0.8204 (tpp) REVERT: C 630 MET cc_start: 0.7280 (tmm) cc_final: 0.6507 (ptm) REVERT: C 828 MET cc_start: 0.7750 (mmt) cc_final: 0.7184 (ppp) REVERT: D 125 MET cc_start: 0.8144 (mmm) cc_final: 0.7919 (mmm) REVERT: D 394 MET cc_start: 0.8054 (mmp) cc_final: 0.7718 (mmp) REVERT: D 512 MET cc_start: 0.8085 (tpp) cc_final: 0.7790 (tpp) REVERT: E 34 MET cc_start: 0.8255 (mmm) cc_final: 0.8011 (mmm) REVERT: E 83 MET cc_start: 0.8814 (mpp) cc_final: 0.8491 (mpp) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.3821 time to fit residues: 88.6795 Evaluate side-chains 127 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 267 optimal weight: 1.9990 chunk 225 optimal weight: 20.0000 chunk 321 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 221 optimal weight: 8.9990 chunk 322 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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** ** 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** C 152 GLN C 335 HIS C 671 GLN C 766 GLN D 696 GLN E 208 ASN ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.028862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.022748 restraints weight = 513225.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.023346 restraints weight = 321874.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.023713 restraints weight = 230094.781| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 27834 Z= 0.114 Angle : 0.536 8.108 37798 Z= 0.277 Chirality : 0.042 0.231 4305 Planarity : 0.004 0.053 4761 Dihedral : 4.000 39.831 3897 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.77 % Favored : 92.94 % Rotamer: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3413 helix: 2.02 (0.14), residues: 1327 sheet: -0.79 (0.26), residues: 437 loop : -1.15 (0.17), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 315 HIS 0.010 0.001 HIS A 85 PHE 0.020 0.001 PHE C 613 TYR 0.025 0.001 TYR D 647 ARG 0.004 0.000 ARG B 755 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 9) link_NAG-ASN : angle 1.89383 ( 27) link_BETA1-4 : bond 0.00662 ( 1) link_BETA1-4 : angle 1.05758 ( 3) hydrogen bonds : bond 0.02911 ( 1130) hydrogen bonds : angle 4.79662 ( 3258) SS BOND : bond 0.00604 ( 14) SS BOND : angle 1.58233 ( 28) covalent geometry : bond 0.00245 (27810) covalent geometry : angle 0.53183 (37740) *********************** 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 131 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.8787 (mpp) cc_final: 0.7788 (mtt) REVERT: A 472 LYS cc_start: 0.9067 (mttt) cc_final: 0.8623 (ptpp) REVERT: A 507 MET cc_start: 0.8800 (ttm) cc_final: 0.8506 (ttp) REVERT: A 788 MET cc_start: 0.9236 (mmm) cc_final: 0.8968 (mmm) REVERT: B 125 MET cc_start: 0.9303 (mmm) cc_final: 0.9056 (mtp) REVERT: B 326 MET cc_start: 0.8112 (mpp) cc_final: 0.7792 (ptt) REVERT: B 512 MET cc_start: 0.8664 (mmp) cc_final: 0.8387 (mmp) REVERT: B 706 MET cc_start: 0.9371 (mtm) cc_final: 0.9147 (mtm) REVERT: B 762 MET cc_start: 0.7130 (mtp) cc_final: 0.6761 (mtp) REVERT: C 133 MET cc_start: 0.9307 (mpp) cc_final: 0.9033 (pmm) REVERT: C 158 MET cc_start: 0.8825 (mtm) cc_final: 0.8369 (mtm) REVERT: C 338 MET cc_start: 0.8379 (tpp) cc_final: 0.7606 (tpp) REVERT: C 630 MET cc_start: 0.7455 (tmm) cc_final: 0.6579 (ptm) REVERT: C 828 MET cc_start: 0.7719 (mmt) cc_final: 0.7194 (ppp) REVERT: D 125 MET cc_start: 0.8127 (mmm) cc_final: 0.7899 (mmm) REVERT: D 394 MET cc_start: 0.8066 (mmp) cc_final: 0.7687 (mmp) REVERT: D 501 MET cc_start: 0.9001 (mmp) cc_final: 0.8381 (mmp) REVERT: D 512 MET cc_start: 0.8001 (tpp) cc_final: 0.7777 (tpp) REVERT: D 706 MET cc_start: 0.9321 (mtp) cc_final: 0.9043 (mtp) REVERT: E 34 MET cc_start: 0.8368 (mmm) cc_final: 0.8081 (mmm) REVERT: E 83 MET cc_start: 0.8744 (mpp) cc_final: 0.8472 (mpp) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.3607 time to fit residues: 79.8282 Evaluate side-chains 123 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 165 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 262 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 126 optimal weight: 0.0070 chunk 137 optimal weight: 0.0570 chunk 332 optimal weight: 9.9990 chunk 5 optimal weight: 0.3980 chunk 170 optimal weight: 6.9990 chunk 308 optimal weight: 20.0000 overall best weight: 2.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.028560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.022486 restraints weight = 515383.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.023050 restraints weight = 326502.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.023455 restraints weight = 236433.278| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27834 Z= 0.126 Angle : 0.535 8.129 37798 Z= 0.277 Chirality : 0.042 0.205 4305 Planarity : 0.003 0.055 4761 Dihedral : 3.974 41.587 3897 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.59 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3413 helix: 1.94 (0.14), residues: 1330 sheet: -0.95 (0.25), residues: 451 loop : -1.15 (0.17), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 198 HIS 0.006 0.001 HIS A 85 PHE 0.025 0.001 PHE B 102 TYR 0.026 0.001 TYR D 647 ARG 0.005 0.000 ARG B 377 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 9) link_NAG-ASN : angle 1.79594 ( 27) link_BETA1-4 : bond 0.00389 ( 1) link_BETA1-4 : angle 1.09941 ( 3) hydrogen bonds : bond 0.02780 ( 1130) hydrogen bonds : angle 4.72150 ( 3258) SS BOND : bond 0.00381 ( 14) SS BOND : angle 1.68675 ( 28) covalent geometry : bond 0.00271 (27810) covalent geometry : angle 0.53115 (37740) *********************** 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: 0 poor density : 130 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8692 (mpp) cc_final: 0.8466 (mpp) REVERT: A 200 MET cc_start: 0.8458 (mtt) cc_final: 0.8090 (mtp) REVERT: A 324 MET cc_start: 0.8719 (mpp) cc_final: 0.7719 (mtt) REVERT: A 472 LYS cc_start: 0.9081 (mttt) cc_final: 0.8683 (ptpp) REVERT: A 507 MET cc_start: 0.8763 (ttm) cc_final: 0.8434 (ttm) REVERT: A 788 MET cc_start: 0.9310 (mmm) cc_final: 0.9078 (mmm) REVERT: B 125 MET cc_start: 0.9320 (mmm) cc_final: 0.9033 (mtp) REVERT: B 240 MET cc_start: 0.8267 (mmm) cc_final: 0.7838 (mmp) REVERT: B 326 MET cc_start: 0.8116 (mpp) cc_final: 0.7889 (ptt) REVERT: B 512 MET cc_start: 0.8639 (mmp) cc_final: 0.8240 (mmp) REVERT: B 762 MET cc_start: 0.7191 (mtp) cc_final: 0.6853 (mtp) REVERT: C 158 MET cc_start: 0.8844 (mtm) cc_final: 0.8369 (mtm) REVERT: C 338 MET cc_start: 0.8402 (tpp) cc_final: 0.7623 (tpp) REVERT: C 630 MET cc_start: 0.7390 (tmm) cc_final: 0.6578 (ptm) REVERT: C 828 MET cc_start: 0.7790 (mmt) cc_final: 0.7208 (ppp) REVERT: D 74 MET cc_start: 0.8986 (tpp) cc_final: 0.8708 (tpt) REVERT: D 326 MET cc_start: 0.9401 (mmm) cc_final: 0.8959 (mmm) REVERT: D 394 MET cc_start: 0.8067 (mmp) cc_final: 0.7630 (mmp) REVERT: D 512 MET cc_start: 0.8081 (tpp) cc_final: 0.7798 (tpp) REVERT: D 634 MET cc_start: 0.9435 (tpp) cc_final: 0.9128 (mmp) REVERT: E 34 MET cc_start: 0.8400 (mmm) cc_final: 0.8186 (mpp) REVERT: E 83 MET cc_start: 0.8727 (mpp) cc_final: 0.8440 (mpp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3665 time to fit residues: 79.6942 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 : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 30.0000 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 326 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 278 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.027954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.021903 restraints weight = 515804.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.022459 restraints weight = 324162.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.022857 restraints weight = 234233.941| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27834 Z= 0.171 Angle : 0.577 8.117 37798 Z= 0.301 Chirality : 0.043 0.187 4305 Planarity : 0.004 0.082 4761 Dihedral : 4.188 45.412 3897 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.82 % Favored : 91.83 % Rotamer: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3413 helix: 1.75 (0.14), residues: 1332 sheet: -1.27 (0.24), residues: 495 loop : -1.15 (0.17), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 390 HIS 0.007 0.001 HIS B 67 PHE 0.029 0.001 PHE D 639 TYR 0.027 0.002 TYR D 647 ARG 0.005 0.001 ARG B 377 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 9) link_NAG-ASN : angle 1.66932 ( 27) link_BETA1-4 : bond 0.01557 ( 1) link_BETA1-4 : angle 1.43228 ( 3) hydrogen bonds : bond 0.02953 ( 1130) hydrogen bonds : angle 4.72446 ( 3258) SS BOND : bond 0.00623 ( 14) SS BOND : angle 1.33077 ( 28) covalent geometry : bond 0.00358 (27810) covalent geometry : angle 0.57491 (37740) *********************** 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 128 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8604 (mtt) cc_final: 0.8338 (mtp) REVERT: A 324 MET cc_start: 0.8840 (mpp) cc_final: 0.7800 (mtt) REVERT: A 472 LYS cc_start: 0.9167 (mttt) cc_final: 0.8820 (ptpp) REVERT: A 507 MET cc_start: 0.8715 (ttm) cc_final: 0.8396 (ttm) REVERT: B 125 MET cc_start: 0.9306 (mmm) cc_final: 0.9028 (mtp) REVERT: B 154 MET cc_start: 0.9176 (tmm) cc_final: 0.7172 (tmm) REVERT: B 240 MET cc_start: 0.8406 (mmm) cc_final: 0.7741 (mmm) REVERT: B 512 MET cc_start: 0.8582 (mmp) cc_final: 0.8170 (mmp) REVERT: B 762 MET cc_start: 0.7261 (mtp) cc_final: 0.6876 (mtp) REVERT: C 133 MET cc_start: 0.9333 (mpp) cc_final: 0.9041 (mpp) REVERT: C 338 MET cc_start: 0.8542 (tpp) cc_final: 0.7652 (tpp) REVERT: C 828 MET cc_start: 0.7709 (mmt) cc_final: 0.7168 (ppp) REVERT: D 394 MET cc_start: 0.8178 (mmp) cc_final: 0.7688 (mmp) REVERT: D 501 MET cc_start: 0.8948 (mmp) cc_final: 0.8174 (mmp) REVERT: D 512 MET cc_start: 0.8062 (tpp) cc_final: 0.7677 (tpp) REVERT: E 34 MET cc_start: 0.8327 (mmm) cc_final: 0.7983 (mmm) REVERT: E 83 MET cc_start: 0.8718 (mpp) cc_final: 0.8427 (mpp) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.3675 time to fit residues: 79.4614 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 : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 313 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 267 optimal weight: 0.3980 chunk 341 optimal weight: 20.0000 chunk 109 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 B 696 GLN ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.027951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.021870 restraints weight = 517842.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.022432 restraints weight = 322554.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.022835 restraints weight = 231822.559| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3461 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= 0.146 Angle : 0.569 11.451 37798 Z= 0.295 Chirality : 0.042 0.181 4305 Planarity : 0.004 0.058 4761 Dihedral : 4.214 42.237 3897 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.44 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3413 helix: 1.64 (0.14), residues: 1332 sheet: -1.28 (0.23), residues: 496 loop : -1.20 (0.17), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 390 HIS 0.006 0.001 HIS C 702 PHE 0.018 0.001 PHE A 253 TYR 0.028 0.001 TYR D 647 ARG 0.005 0.000 ARG C 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00714 ( 9) link_NAG-ASN : angle 1.67640 ( 27) link_BETA1-4 : bond 0.00526 ( 1) link_BETA1-4 : angle 1.10321 ( 3) hydrogen bonds : bond 0.02908 ( 1130) hydrogen bonds : angle 4.72849 ( 3258) SS BOND : bond 0.00374 ( 14) SS BOND : angle 1.52549 ( 28) covalent geometry : bond 0.00312 (27810) covalent geometry : angle 0.56561 (37740) *********************** 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 : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8854 (mpp) cc_final: 0.8582 (mpp) REVERT: A 324 MET cc_start: 0.8805 (mpp) cc_final: 0.7665 (mtt) REVERT: A 472 LYS cc_start: 0.9186 (mttt) cc_final: 0.8736 (ptpp) REVERT: B 125 MET cc_start: 0.9340 (mmm) cc_final: 0.9064 (mtp) REVERT: B 240 MET cc_start: 0.8441 (mmm) cc_final: 0.7764 (mmm) REVERT: B 512 MET cc_start: 0.8633 (mmp) cc_final: 0.8199 (mmp) REVERT: B 762 MET cc_start: 0.7403 (mtp) cc_final: 0.7087 (mtp) REVERT: C 133 MET cc_start: 0.9317 (mpp) cc_final: 0.8992 (mpp) REVERT: C 158 MET cc_start: 0.8829 (mtm) cc_final: 0.8580 (mtm) REVERT: C 630 MET cc_start: 0.7247 (tmm) cc_final: 0.6420 (ptm) REVERT: C 828 MET cc_start: 0.7659 (mmt) cc_final: 0.7100 (ppp) REVERT: D 125 MET cc_start: 0.8117 (mmm) cc_final: 0.7837 (mmm) REVERT: D 394 MET cc_start: 0.8124 (mmp) cc_final: 0.7711 (mmp) REVERT: D 501 MET cc_start: 0.9002 (mmp) cc_final: 0.8310 (mmp) REVERT: D 512 MET cc_start: 0.8091 (tpp) cc_final: 0.7702 (tpp) REVERT: E 34 MET cc_start: 0.8440 (mmm) cc_final: 0.7922 (mmm) REVERT: E 83 MET cc_start: 0.8703 (mpp) cc_final: 0.8379 (mpp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3701 time to fit residues: 79.0922 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 : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 342 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 270 optimal weight: 0.8980 chunk 247 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 214 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 299 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 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 = 0.3205 r_free = 0.3205 target = 0.028200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.022093 restraints weight = 513490.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.022651 restraints weight = 322905.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.023058 restraints weight = 232168.090| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27834 Z= 0.109 Angle : 0.556 10.570 37798 Z= 0.286 Chirality : 0.043 0.289 4305 Planarity : 0.003 0.059 4761 Dihedral : 4.094 40.197 3897 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.65 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3413 helix: 1.64 (0.14), residues: 1334 sheet: -1.19 (0.24), residues: 465 loop : -1.24 (0.17), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 167 HIS 0.005 0.001 HIS B 38 PHE 0.023 0.001 PHE B 321 TYR 0.028 0.001 TYR D 647 ARG 0.003 0.000 ARG C 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 9) link_NAG-ASN : angle 1.62228 ( 27) link_BETA1-4 : bond 0.00636 ( 1) link_BETA1-4 : angle 1.49846 ( 3) hydrogen bonds : bond 0.02727 ( 1130) hydrogen bonds : angle 4.60469 ( 3258) SS BOND : bond 0.00349 ( 14) SS BOND : angle 1.58122 ( 28) covalent geometry : bond 0.00237 (27810) covalent geometry : angle 0.55336 (37740) *********************** 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 124 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8886 (mpp) cc_final: 0.8550 (mpp) REVERT: A 324 MET cc_start: 0.8763 (mpp) cc_final: 0.7584 (mtt) REVERT: A 472 LYS cc_start: 0.9164 (mttt) cc_final: 0.8688 (ptpp) REVERT: B 125 MET cc_start: 0.9269 (mmm) cc_final: 0.9067 (mtp) REVERT: B 240 MET cc_start: 0.8466 (mmm) cc_final: 0.7833 (mmm) REVERT: B 512 MET cc_start: 0.8640 (mmp) cc_final: 0.8168 (mmp) REVERT: C 133 MET cc_start: 0.9311 (mpp) cc_final: 0.8948 (mpp) REVERT: C 158 MET cc_start: 0.8793 (mtm) cc_final: 0.8537 (mtm) REVERT: C 338 MET cc_start: 0.8492 (tpp) cc_final: 0.7646 (tpp) REVERT: C 630 MET cc_start: 0.7536 (tmm) cc_final: 0.6510 (ptm) REVERT: C 788 MET cc_start: 0.8978 (mmm) cc_final: 0.8538 (mmm) REVERT: C 828 MET cc_start: 0.7644 (mmt) cc_final: 0.7088 (ppp) REVERT: D 74 MET cc_start: 0.9079 (tpp) cc_final: 0.8772 (mmm) REVERT: D 394 MET cc_start: 0.8147 (mmp) cc_final: 0.7740 (mmp) REVERT: D 501 MET cc_start: 0.8932 (mmp) cc_final: 0.8334 (mmp) REVERT: D 512 MET cc_start: 0.8103 (tpp) cc_final: 0.7703 (tpp) REVERT: E 34 MET cc_start: 0.8510 (mmm) cc_final: 0.7981 (mmm) REVERT: E 83 MET cc_start: 0.8674 (mpp) cc_final: 0.8320 (mpp) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3829 time to fit residues: 80.2846 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 : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 266 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 79 optimal weight: 0.0980 chunk 330 optimal weight: 9.9990 chunk 336 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 287 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.027841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.021754 restraints weight = 517982.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.022316 restraints weight = 323580.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.022711 restraints weight = 233247.485| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27834 Z= 0.147 Angle : 0.570 9.111 37798 Z= 0.295 Chirality : 0.043 0.248 4305 Planarity : 0.004 0.059 4761 Dihedral : 4.222 40.579 3897 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.76 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3413 helix: 1.59 (0.14), residues: 1331 sheet: -1.25 (0.24), residues: 501 loop : -1.24 (0.17), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 372 HIS 0.004 0.001 HIS A 119 PHE 0.026 0.001 PHE A 145 TYR 0.027 0.001 TYR D 647 ARG 0.007 0.000 ARG C 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 9) link_NAG-ASN : angle 1.64677 ( 27) link_BETA1-4 : bond 0.00527 ( 1) link_BETA1-4 : angle 1.30077 ( 3) hydrogen bonds : bond 0.02893 ( 1130) hydrogen bonds : angle 4.64882 ( 3258) SS BOND : bond 0.00319 ( 14) SS BOND : angle 1.24598 ( 28) covalent geometry : bond 0.00316 (27810) covalent geometry : angle 0.56791 (37740) *********************** 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 123 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.8800 (mpp) cc_final: 0.7930 (mtt) REVERT: A 472 LYS cc_start: 0.9190 (mttt) cc_final: 0.8751 (ptpp) REVERT: B 125 MET cc_start: 0.9280 (mmm) cc_final: 0.9078 (mtp) REVERT: C 133 MET cc_start: 0.9320 (mpp) cc_final: 0.8970 (mpp) REVERT: C 630 MET cc_start: 0.7373 (tmm) cc_final: 0.6527 (ptm) REVERT: C 828 MET cc_start: 0.7615 (mmt) cc_final: 0.7148 (ptp) REVERT: D 354 MET cc_start: 0.8820 (mmp) cc_final: 0.7075 (mmp) REVERT: D 394 MET cc_start: 0.8196 (mmp) cc_final: 0.7754 (mmp) REVERT: D 512 MET cc_start: 0.8110 (tpp) cc_final: 0.7740 (tpp) REVERT: E 34 MET cc_start: 0.8444 (mmm) cc_final: 0.7895 (mmm) REVERT: E 83 MET cc_start: 0.8584 (mpp) cc_final: 0.8220 (mpp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.3614 time to fit residues: 75.2183 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 : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 303 optimal weight: 20.0000 chunk 290 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 chunk 122 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- 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 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 HIS D 293 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.028681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.020743 restraints weight = 494547.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.021283 restraints weight = 333269.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.021685 restraints weight = 255154.650| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27834 Z= 0.192 Angle : 0.629 8.881 37798 Z= 0.328 Chirality : 0.044 0.212 4305 Planarity : 0.004 0.059 4761 Dihedral : 4.560 44.112 3897 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.67 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3413 helix: 1.39 (0.14), residues: 1330 sheet: -1.48 (0.23), residues: 518 loop : -1.32 (0.17), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 390 HIS 0.005 0.001 HIS C 85 PHE 0.025 0.002 PHE A 253 TYR 0.028 0.002 TYR D 647 ARG 0.004 0.001 ARG C 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 9) link_NAG-ASN : angle 1.71771 ( 27) link_BETA1-4 : bond 0.00764 ( 1) link_BETA1-4 : angle 1.49959 ( 3) hydrogen bonds : bond 0.03239 ( 1130) hydrogen bonds : angle 4.81046 ( 3258) SS BOND : bond 0.00493 ( 14) SS BOND : angle 1.63183 ( 28) covalent geometry : bond 0.00408 (27810) covalent geometry : angle 0.62653 (37740) *********************** 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 123 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.8937 (mpp) cc_final: 0.8143 (mtt) REVERT: A 472 LYS cc_start: 0.9235 (mttt) cc_final: 0.8846 (ptpp) REVERT: B 125 MET cc_start: 0.9381 (mmm) cc_final: 0.9081 (mtp) REVERT: B 237 MET cc_start: 0.9219 (tmm) cc_final: 0.8998 (tmm) REVERT: B 240 MET cc_start: 0.7836 (tpp) cc_final: 0.7049 (mmm) REVERT: B 326 MET cc_start: 0.8390 (mpp) cc_final: 0.8173 (ppp) REVERT: B 512 MET cc_start: 0.8473 (mmp) cc_final: 0.7978 (mmp) REVERT: B 762 MET cc_start: 0.7270 (mtp) cc_final: 0.6791 (mtp) REVERT: C 133 MET cc_start: 0.9181 (mpp) cc_final: 0.8790 (mpp) REVERT: C 338 MET cc_start: 0.8654 (tpp) cc_final: 0.7743 (tpp) REVERT: C 630 MET cc_start: 0.7420 (tmm) cc_final: 0.6533 (ptm) REVERT: D 394 MET cc_start: 0.8383 (mmp) cc_final: 0.7835 (mmp) REVERT: D 501 MET cc_start: 0.9003 (mmp) cc_final: 0.8107 (mmp) REVERT: D 512 MET cc_start: 0.8028 (tpp) cc_final: 0.7689 (tpp) REVERT: E 34 MET cc_start: 0.8557 (mmm) cc_final: 0.7974 (mmm) REVERT: E 83 MET cc_start: 0.8714 (mpp) cc_final: 0.8350 (mpp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.3486 time to fit residues: 72.8831 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 : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 10 optimal weight: 7.9990 chunk 286 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 305 optimal weight: 8.9990 chunk 249 optimal weight: 0.0670 chunk 236 optimal weight: 5.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.027651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.021847 restraints weight = 515687.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.022380 restraints weight = 327016.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.022761 restraints weight = 236358.838| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27834 Z= 0.129 Angle : 0.593 8.869 37798 Z= 0.305 Chirality : 0.043 0.187 4305 Planarity : 0.004 0.058 4761 Dihedral : 4.428 43.465 3897 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.91 % Favored : 91.74 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3413 helix: 1.42 (0.14), residues: 1336 sheet: -1.42 (0.23), residues: 501 loop : -1.30 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 390 HIS 0.005 0.001 HIS C 168 PHE 0.025 0.001 PHE A 253 TYR 0.028 0.001 TYR D 647 ARG 0.003 0.000 ARG C 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 9) link_NAG-ASN : angle 1.71698 ( 27) link_BETA1-4 : bond 0.00528 ( 1) link_BETA1-4 : angle 1.77720 ( 3) hydrogen bonds : bond 0.02946 ( 1130) hydrogen bonds : angle 4.69005 ( 3258) SS BOND : bond 0.00363 ( 14) SS BOND : angle 1.65769 ( 28) covalent geometry : bond 0.00280 (27810) covalent geometry : angle 0.59011 (37740) ********************** 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 122 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.8818 (mpp) cc_final: 0.8566 (mpp) REVERT: A 306 MET cc_start: 0.7756 (tpp) cc_final: 0.7502 (tpp) REVERT: A 324 MET cc_start: 0.8804 (mpp) cc_final: 0.7948 (mtt) REVERT: A 331 MET cc_start: 0.2735 (tpt) cc_final: 0.2484 (tpt) REVERT: A 472 LYS cc_start: 0.9227 (mttt) cc_final: 0.8816 (ptpp) REVERT: B 125 MET cc_start: 0.9269 (mmm) cc_final: 0.9019 (mtp) REVERT: B 240 MET cc_start: 0.7792 (tpp) cc_final: 0.7064 (mmm) REVERT: B 326 MET cc_start: 0.8316 (mpp) cc_final: 0.8057 (ppp) REVERT: B 512 MET cc_start: 0.8456 (mmp) cc_final: 0.7942 (mmp) REVERT: B 762 MET cc_start: 0.7314 (mtp) cc_final: 0.6835 (mtp) REVERT: C 133 MET cc_start: 0.9337 (mpp) cc_final: 0.8956 (mpp) REVERT: C 200 MET cc_start: 0.9143 (tmm) cc_final: 0.8675 (tmm) REVERT: C 630 MET cc_start: 0.7383 (tmm) cc_final: 0.6522 (ptm) REVERT: C 828 MET cc_start: 0.7606 (mmt) cc_final: 0.7144 (ptp) REVERT: D 354 MET cc_start: 0.8853 (mmp) cc_final: 0.7108 (mmp) REVERT: D 394 MET cc_start: 0.8368 (mmp) cc_final: 0.7786 (mmp) REVERT: D 501 MET cc_start: 0.8947 (mmp) cc_final: 0.8001 (mmp) REVERT: D 512 MET cc_start: 0.7990 (tpp) cc_final: 0.7615 (tpp) REVERT: E 34 MET cc_start: 0.8639 (mmm) cc_final: 0.8413 (mmp) REVERT: E 83 MET cc_start: 0.8571 (mpp) cc_final: 0.8186 (mpp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.3463 time to fit residues: 71.9659 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 : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 153 optimal weight: 20.0000 chunk 166 optimal weight: 0.8980 chunk 152 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 343 optimal weight: 40.0000 chunk 84 optimal weight: 9.9990 chunk 317 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 199 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** F 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.028692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.020772 restraints weight = 493565.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.021324 restraints weight = 331532.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.021716 restraints weight = 251995.278| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27834 Z= 0.172 Angle : 0.617 8.700 37798 Z= 0.319 Chirality : 0.043 0.187 4305 Planarity : 0.004 0.060 4761 Dihedral : 4.564 44.534 3897 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.97 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3413 helix: 1.39 (0.14), residues: 1329 sheet: -1.54 (0.23), residues: 511 loop : -1.33 (0.17), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 390 HIS 0.006 0.001 HIS C 168 PHE 0.026 0.001 PHE A 253 TYR 0.027 0.002 TYR D 647 ARG 0.003 0.000 ARG B 844 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 9) link_NAG-ASN : angle 1.74883 ( 27) link_BETA1-4 : bond 0.00577 ( 1) link_BETA1-4 : angle 1.58353 ( 3) hydrogen bonds : bond 0.03123 ( 1130) hydrogen bonds : angle 4.76962 ( 3258) SS BOND : bond 0.00323 ( 14) SS BOND : angle 1.41030 ( 28) covalent geometry : bond 0.00367 (27810) covalent geometry : angle 0.61388 (37740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7452.53 seconds wall clock time: 132 minutes 57.26 seconds (7977.26 seconds total)