Starting phenix.real_space_refine on Thu Mar 5 16:57:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6whv_21677/03_2026/6whv_21677.cif Found real_map, /net/cci-nas-00/data/ceres_data/6whv_21677/03_2026/6whv_21677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6whv_21677/03_2026/6whv_21677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6whv_21677/03_2026/6whv_21677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6whv_21677/03_2026/6whv_21677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6whv_21677/03_2026/6whv_21677.map" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.860 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 145 5.16 5 Cl 6 4.86 5 C 15238 2.51 5 N 3863 2.21 5 O 4510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23764 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 5936 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 35, 'TRANS': 767} Chain breaks: 3 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 22, 'HIS:plan': 4, 'GLU:plan': 16, 'GLN:plan1': 8, 'PHE:plan': 3, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 288 Chain: "B" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5697 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PTRANS': 27, 'TRANS': 755} Chain breaks: 2 Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 602 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 14, 'HIS:plan': 5, 'GLU:plan': 18, 'PHE:plan': 5, 'ARG:plan': 12, 'GLN:plan1': 8, 'TYR:plan': 4, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 301 Chain: "C" Number of atoms: 6040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 6040 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 35, 'TRANS': 764} Chain breaks: 3 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 18, 'HIS:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 165 Chain: "D" Number of atoms: 5930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5930 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 28, 'TRANS': 755} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 238 Planarities with less than four sites: {'ASP:plan': 7, 'HIS:plan': 2, 'GLU:plan': 12, 'PHE:plan': 4, 'ARG:plan': 9, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 163 Chain: "E" 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: "A" 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: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.25, per 1000 atoms: 0.26 Number of scatterers: 23764 At special positions: 0 Unit cell: (137, 149.33, 189.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 6 17.00 S 145 16.00 P 2 15.00 O 4510 8.00 N 3863 7.00 C 15238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.04 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.02 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.04 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.04 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.04 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=5, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1001 " - " ASN A 297 " " NAG B 902 " - " ASN B 542 " " NAG D 902 " - " ASN D 542 " " NAG D 903 " - " ASN D 688 " " NAG E 1 " - " ASN B 341 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QGM C1001 " Number of C-beta restraints generated: 5920 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 33 sheets defined 41.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 37 through 52 Processing helix chain 'A' and resid 71 through 83 removed outlier: 3.600A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.230A pdb=" N ILE A 116 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.588A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 147 through 156 removed outlier: 4.100A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 4.032A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.536A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.751A pdb=" N ALA A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.600A pdb=" N LEU A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 276 through 281' Processing helix chain 'A' and resid 299 through 317 removed outlier: 3.847A pdb=" N SER A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 479 through 492 removed outlier: 3.540A pdb=" N ARG A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 542 through 548 removed outlier: 3.752A pdb=" N TYR A 547 " --> pdb=" O ARG A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 603 removed outlier: 3.597A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 634 removed outlier: 3.724A pdb=" N VAL A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 648 through 679 removed outlier: 4.220A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 removed outlier: 3.517A pdb=" N LEU A 693 " --> pdb=" O ASP A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'A' and resid 720 through 729 removed outlier: 3.566A pdb=" N HIS A 726 " --> pdb=" O THR A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.583A pdb=" N ALA A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 3.722A pdb=" N LYS A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 800 Processing helix chain 'A' and resid 804 through 814 removed outlier: 3.687A pdb=" N LYS A 811 " --> pdb=" O GLU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 861 removed outlier: 4.418A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL A 841 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 842 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 843 " --> pdb=" O MET A 839 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS A 861 " --> pdb=" O ALA A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 removed outlier: 3.903A pdb=" N ILE B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 107 through 118 removed outlier: 3.630A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 163 Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 210 through 217 removed outlier: 3.841A pdb=" N SER B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.570A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 473 removed outlier: 3.792A pdb=" N LYS B 466 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 removed outlier: 4.355A pdb=" N VAL B 501 " --> pdb=" O MET B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 523 removed outlier: 4.177A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 578 removed outlier: 3.949A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 removed outlier: 3.832A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 652 removed outlier: 4.211A pdb=" N VAL B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 removed outlier: 4.008A pdb=" N ARG B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 696 Processing helix chain 'B' and resid 699 through 709 Processing helix chain 'B' and resid 714 through 723 removed outlier: 3.690A pdb=" N THR B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.524A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 742 " --> pdb=" O TYR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 786 removed outlier: 3.823A pdb=" N ASP B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.676A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 843 removed outlier: 3.990A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 51 removed outlier: 3.591A pdb=" N PHE C 42 " --> pdb=" O HIS C 38 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 73 through 82 Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.818A pdb=" N THR C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 106 through 111' Processing helix chain 'C' and resid 112 through 115 removed outlier: 4.157A pdb=" N ARG C 115 " --> pdb=" O GLY C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 115' Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.567A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 130' Processing helix chain 'C' and resid 146 through 155 removed outlier: 3.832A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 removed outlier: 3.953A pdb=" N ALA C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 235 removed outlier: 4.004A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 removed outlier: 4.158A pdb=" N THR C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 275 Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 297 through 318 removed outlier: 4.209A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HIS C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 402 through 406 removed outlier: 3.637A pdb=" N GLY C 405 " --> pdb=" O TRP C 402 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 406 " --> pdb=" O PRO C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 402 through 406' Processing helix chain 'C' and resid 479 through 492 Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.781A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 604 removed outlier: 4.235A pdb=" N TRP C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 603 " --> pdb=" O TYR C 599 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.599A pdb=" N TRP C 632 " --> pdb=" O MET C 628 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 678 removed outlier: 3.782A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 678 " --> pdb=" O ALA C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 removed outlier: 3.591A pdb=" N ASN C 695 " --> pdb=" O PRO C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 717 removed outlier: 4.054A pdb=" N GLN C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 729 removed outlier: 4.299A pdb=" N HIS C 726 " --> pdb=" O THR C 722 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 729 " --> pdb=" O ARG C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 743 removed outlier: 3.519A pdb=" N ALA C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 761 removed outlier: 5.265A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 removed outlier: 3.701A pdb=" N LEU C 798 " --> pdb=" O SER C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 814 removed outlier: 4.770A pdb=" N LYS C 811 " --> pdb=" O GLU C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 861 removed outlier: 3.511A pdb=" N MET C 834 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLY C 836 " --> pdb=" O GLU C 832 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL C 837 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE C 838 " --> pdb=" O MET C 834 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 841 " --> pdb=" O VAL C 837 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 58 removed outlier: 4.181A pdb=" N LYS D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP D 58 " --> pdb=" O HIS D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 107 through 118 removed outlier: 4.258A pdb=" N ILE D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.529A pdb=" N GLN D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 192 Processing helix chain 'D' and resid 211 through 222 removed outlier: 3.557A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 245 Processing helix chain 'D' and resid 288 through 309 removed outlier: 3.836A pdb=" N ARG D 292 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.171A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 341 removed outlier: 4.215A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 495 through 503 removed outlier: 3.644A pdb=" N VAL D 501 " --> pdb=" O MET D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 548 through 552 removed outlier: 3.538A pdb=" N LEU D 551 " --> pdb=" O SER D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 578 removed outlier: 4.292A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 Processing helix chain 'D' and resid 628 through 651 removed outlier: 4.080A pdb=" N VAL D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 removed outlier: 3.655A pdb=" N ARG D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 677 removed outlier: 4.069A pdb=" N PHE D 677 " --> pdb=" O PRO D 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 674 through 677' Processing helix chain 'D' and resid 689 through 694 Processing helix chain 'D' and resid 700 through 706 Processing helix chain 'D' and resid 714 through 721 Processing helix chain 'D' and resid 733 through 740 removed outlier: 4.783A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 772 through 786 Processing helix chain 'D' and resid 788 through 796 Processing helix chain 'D' and resid 814 through 844 removed outlier: 3.751A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 819 " --> pdb=" O ILE D 815 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 64 removed outlier: 5.543A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ASN A 28 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N LEU A 91 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 215 removed outlier: 7.077A pdb=" N ILE A 163 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 215 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 165 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A 239 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 361 removed outlier: 3.790A pdb=" N GLU A 360 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 389 Processing sheet with id=AA5, first strand: chain 'A' and resid 494 through 498 removed outlier: 3.534A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 535 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 782 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA A 536 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLY A 780 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 538 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY A 778 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N SER A 777 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LYS A 555 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N PHE A 779 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE A 781 " --> pdb=" O SER A 551 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 432 removed outlier: 3.539A pdb=" N TYR A 477 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 458 through 459 Processing sheet with id=AA8, first strand: chain 'A' and resid 559 through 561 removed outlier: 3.850A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 563 through 564 removed outlier: 3.706A pdb=" N VAL A 563 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 768 " --> pdb=" O VAL A 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 73 removed outlier: 7.434A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 256 through 257 removed outlier: 6.421A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 279 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 362 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP B 379 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AB4, first strand: chain 'B' and resid 434 through 435 removed outlier: 3.682A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 530 through 532 removed outlier: 4.007A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 532 " --> pdb=" O THR B 760 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 534 through 536 Processing sheet with id=AB7, first strand: chain 'B' and resid 656 through 657 removed outlier: 3.795A pdb=" N GLN B 656 " --> pdb=" O VAL B 808 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.752A pdb=" N VAL C 27 " --> pdb=" O GLN C 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.873A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 240 through 242 removed outlier: 6.101A pdb=" N ILE C 240 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TRP C 268 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 385 " --> pdb=" O ILE C 374 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.042A pdb=" N GLU C 360 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 497 through 498 removed outlier: 6.547A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.521A pdb=" N CYS C 476 " --> pdb=" O VAL C 455 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 508 through 511 removed outlier: 4.259A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 702 through 703 removed outlier: 3.560A pdb=" N ALA C 703 " --> pdb=" O ALA C 749 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE C 751 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE C 561 " --> pdb=" O THR C 770 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR C 770 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 563 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 768 " --> pdb=" O VAL C 563 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 66 through 72 removed outlier: 6.583A pdb=" N ILE D 35 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLU D 69 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE D 37 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 171 through 173 removed outlier: 3.554A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE D 228 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER D 279 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AD1, first strand: chain 'D' and resid 478 through 480 removed outlier: 6.493A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 434 through 436 removed outlier: 3.663A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AD4, first strand: chain 'D' and resid 534 through 535 Processing sheet with id=AD5, first strand: chain 'D' and resid 537 through 538 removed outlier: 3.620A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 683 through 684 830 hydrogen bonds defined for protein. 2385 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: 4.48 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3984 1.31 - 1.44: 6492 1.44 - 1.57: 13552 1.57 - 1.70: 3 1.70 - 1.83: 253 Bond restraints: 24284 Sorted by residual: bond pdb=" C1 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.851 1.624 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.851 1.645 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" N QGM C1001 " pdb=" CAV QGM C1001 " ideal model delta sigma weight residual 1.347 1.482 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" O3 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.629 1.495 0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" O3 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.629 1.496 0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 24279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 31979 2.04 - 4.08: 1022 4.08 - 6.12: 121 6.12 - 8.16: 22 8.16 - 10.20: 7 Bond angle restraints: 33151 Sorted by residual: angle pdb=" N GLY B 129 " pdb=" CA GLY B 129 " pdb=" C GLY B 129 " ideal model delta sigma weight residual 114.66 105.10 9.56 1.24e+00 6.50e-01 5.95e+01 angle pdb=" C THR C 812 " pdb=" N TRP C 813 " pdb=" CA TRP C 813 " ideal model delta sigma weight residual 121.52 113.26 8.26 1.74e+00 3.30e-01 2.25e+01 angle pdb=" N SER B 170 " pdb=" CA SER B 170 " pdb=" C SER B 170 " ideal model delta sigma weight residual 110.24 115.64 -5.40 1.30e+00 5.92e-01 1.73e+01 angle pdb=" C TRP C 813 " pdb=" N VAL C 814 " pdb=" CA VAL C 814 " ideal model delta sigma weight residual 122.77 118.88 3.89 1.05e+00 9.07e-01 1.37e+01 angle pdb=" C THR A 830 " pdb=" N CYS A 831 " pdb=" CA CYS A 831 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 ... (remaining 33146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 12782 17.66 - 35.32: 1293 35.32 - 52.97: 225 52.97 - 70.63: 42 70.63 - 88.29: 30 Dihedral angle restraints: 14372 sinusoidal: 5190 harmonic: 9182 Sorted by residual: dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 321 " pdb=" CB CYS B 321 " ideal model delta sinusoidal sigma weight residual -86.00 -2.18 -83.82 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CB CYS D 86 " pdb=" SG CYS D 86 " pdb=" SG CYS D 321 " pdb=" CB CYS D 321 " ideal model delta sinusoidal sigma weight residual -86.00 -5.64 -80.36 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS B 429 " pdb=" SG CYS B 429 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual 93.00 171.23 -78.23 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 14369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.882: 3893 0.882 - 1.764: 0 1.764 - 2.645: 0 2.645 - 3.527: 0 3.527 - 4.409: 1 Chirality restraints: 3894 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 2.01 -4.41 2.00e-02 2.50e+03 4.86e+04 chirality pdb=" CG QGM C1001 " pdb=" CB QGM C1001 " pdb=" CD1 QGM C1001 " pdb=" ND2 QGM C1001 " both_signs ideal model delta sigma weight residual False -2.43 -2.67 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA THR C 103 " pdb=" N THR C 103 " pdb=" C THR C 103 " pdb=" CB THR C 103 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 3891 not shown) Planarity restraints: 4226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 825 " 0.056 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO A 826 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 826 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 826 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 679 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO D 680 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 680 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 680 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 414 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO D 415 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 415 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 415 " -0.032 5.00e-02 4.00e+02 ... (remaining 4223 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 587 2.64 - 3.21: 25227 3.21 - 3.77: 35255 3.77 - 4.34: 45601 4.34 - 4.90: 68912 Nonbonded interactions: 175582 Sorted by model distance: nonbonded pdb=" O VAL D 243 " pdb=" OG SER D 246 " model vdw 2.076 3.040 nonbonded pdb=" O ASP B 113 " pdb=" OG SER B 116 " model vdw 2.079 3.040 nonbonded pdb=" OG SER D 34 " pdb=" O VAL D 65 " model vdw 2.115 3.040 nonbonded pdb=" OH TYR D 507 " pdb=" OG SER D 770 " model vdw 2.137 3.040 nonbonded pdb=" OG SER D 352 " pdb=" OD1 ASP D 354 " model vdw 2.141 3.040 ... (remaining 175577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 98 or (resid 99 through 102 and (name N or name \ CA or name C or name O or name CB )) or resid 103 through 114 or (resid 115 and \ (name N or name CA or name C or name O or name CB )) or resid 116 through 169 o \ r (resid 170 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 71 or (resid 172 and (name N or name CA or name C or name O or name CB )) or res \ id 173 through 190 or resid 207 through 210 or (resid 211 through 212 and (name \ N or name CA or name C or name O or name CB )) or resid 213 through 222 or (resi \ d 223 and (name N or name CA or name C or name O or name CB )) or resid 224 thro \ ugh 271 or (resid 272 and (name N or name CA or name C or name O or name CB )) o \ r resid 273 or (resid 274 and (name N or name CA or name C or name O or name CB \ )) or resid 275 through 280 or (resid 281 and (name N or name CA or name C or na \ me O or name CB )) or resid 282 through 295 or (resid 296 and (name N or name CA \ or name C or name O or name CB )) or resid 297 through 320 or (resid 321 and (n \ ame N or name CA or name C or name O or name CB )) or resid 322 through 435 or ( \ resid 436 and (name N or name CA or name C or name O or name CB )) or resid 437 \ through 441 or (resid 442 and (name N or name CA or name C or name O or name CB \ )) or resid 443 through 512 or (resid 513 and (name N or name CA or name C or na \ me O or name CB )) or resid 514 through 515 or (resid 516 through 517 and (name \ N or name CA or name C or name O or name CB )) or resid 518 through 568 or (resi \ d 569 and (name N or name CA or name C or name O or name CB )) or resid 570 thro \ ugh 839 or (resid 840 and (name N or name CA or name C or name O or name CB )) o \ r resid 841 through 850 or (resid 851 and (name N or name CA or name C or name O \ or name CB )) or resid 852 through 862)) selection = (chain 'C' and (resid 25 through 38 or (resid 39 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 47 or (resid 48 through \ 49 and (name N or name CA or name C or name O or name CB )) or resid 50 or (res \ id 51 through 52 and (name N or name CA or name C or name O or name CB )) or res \ id 58 or (resid 59 and (name N or name CA or name C or name O or name CB )) or r \ esid 60 or (resid 61 through 62 and (name N or name CA or name C or name O or na \ me CB )) or resid 63 through 152 or (resid 153 and (name N or name CA or name C \ or name O or name CB )) or resid 154 through 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 through 185 or (resid 186 t \ hrough 188 and (name N or name CA or name C or name O or name CB )) or resid 189 \ through 213 or (resid 214 and (name N or name CA or name C or name O or name CB \ )) or resid 215 through 232 or (resid 233 and (name N or name CA or name C or n \ ame O or name CB )) or resid 234 through 235 or (resid 236 through 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 297 or (res \ id 298 and (name N or name CA or name C or name O or name CB )) or resid 299 thr \ ough 310 or (resid 311 through 312 and (name N or name CA or name C or name O or \ name CB )) or resid 313 through 314 or (resid 315 and (name N or name CA or nam \ e C or name O or name CB )) or resid 316 through 317 or (resid 318 through 321 a \ nd (name N or name CA or name C or name O or name CB )) or resid 322 through 346 \ or (resid 347 and (name N or name CA or name C or name O or name CB )) or resid \ 348 through 349 or (resid 350 and (name N or name CA or name C or name O or nam \ e CB )) or resid 351 through 357 or (resid 358 and (name N or name CA or name C \ or name O or name CB )) or resid 359 through 361 or (resid 362 through 364 and ( \ name N or name CA or name C or name O or name CB )) or resid 365 through 366 or \ (resid 367 through 368 and (name N or name CA or name C or name O or name CB )) \ or resid 369 through 387 or (resid 388 and (name N or name CA or name C or name \ O or name CB )) or resid 389 through 395 or (resid 396 through 399 and (name N o \ r name CA or name C or name O or name CB )) or resid 400 through 405 or (resid 4 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 407 through \ 461 or (resid 462 and (name N or name CA or name C or name O or name CB )) or r \ esid 463 through 495 or (resid 496 and (name N or name CA or name C or name O or \ name CB )) or resid 497 through 516 or (resid 517 and (name N or name CA or nam \ e C or name O or name CB )) or resid 518 through 524 or (resid 525 and (name N o \ r name CA or name C or name O or name CB )) or resid 526 through 563 or (resid 5 \ 64 through 565 and (name N or name CA or name C or name O or name CB )) or resid \ 566 through 691 or (resid 692 and (name N or name CA or name C or name O or nam \ e CB )) or resid 693 through 706 or (resid 707 and (name N or name CA or name C \ or name O or name CB )) or resid 708 through 762 or (resid 763 through 764 and ( \ name N or name CA or name C or name O or name CB )) or resid 765 through 774 or \ (resid 775 and (name N or name CA or name C or name O or name CB )) or resid 776 \ through 814 or (resid 815 and (name N or name CA or name C or name O or name CB \ )) or resid 816 through 862)) } ncs_group { reference = (chain 'B' and (resid 35 through 206 or (resid 207 and (name N or name CA or nam \ e C or name O or name CB )) or resid 208 through 210 or (resid 211 and (name N o \ r name CA or name C or name O or name CB )) or resid 212 or (resid 213 and (name \ N or name CA or name C or name O or name CB )) or resid 214 through 285 or (res \ id 286 and (name N or name CA or name C or name O or name CB )) or resid 287 thr \ ough 293 or (resid 294 and (name N or name CA or name C or name O or name CB )) \ or resid 295 through 309 or (resid 310 and (name N or name CA or name C or name \ O or name CB )) or resid 311 through 393 or (resid 394 and (name N or name CA or \ name C or name O or name CB )) or resid 404 through 438 or (resid 439 and (name \ N or name CA or name C or name O or name CB )) or resid 440 through 444 or resi \ d 447 through 504 or (resid 505 through 506 and (name N or name CA or name C or \ name O or name CB )) or resid 507 through 576 or (resid 577 and (name N or name \ CA or name C or name O or name CB )) or resid 578 through 603 or (resid 604 thro \ ugh 605 and (name N or name CA or name C or name O or name CB )) or resid 606 th \ rough 841 or (resid 842 and (name N or name CA or name C or name O or name CB )) \ or resid 843 through 902)) selection = (chain 'D' and (resid 35 through 57 or (resid 58 through 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 74 or (resid 75 and (na \ me N or name CA or name C or name O or name CB )) or resid 76 through 78 or (res \ id 79 and (name N or name CA or name C or name O or name CB )) or resid 80 throu \ gh 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) or r \ esid 86 or (resid 87 through 89 and (name N or name CA or name C or name O or na \ me CB )) or resid 90 or (resid 91 through 94 and (name N or name CA or name C or \ name O or name CB )) or resid 95 through 100 or (resid 101 and (name N or name \ CA or name C or name O or name CB )) or resid 102 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 through 135 or \ (resid 136 through 139 and (name N or name CA or name C or name O or name CB )) \ or resid 140 or (resid 141 and (name N or name CA or name C or name O or name C \ B )) or resid 142 through 169 or (resid 170 and (name N or name CA or name C or \ name O or name CB )) or resid 171 through 200 or (resid 201 and (name N or name \ CA or name C or name O or name CB )) or resid 202 through 216 or (resid 217 and \ (name N or name CA or name C or name O or name CB )) or resid 218 through 222 or \ (resid 223 through 224 and (name N or name CA or name C or name O or name CB )) \ or resid 225 through 233 or (resid 234 and (name N or name CA or name C or name \ O or name CB )) or resid 235 through 251 or (resid 252 and (name N or name CA o \ r name C or name O or name CB )) or resid 253 through 312 or (resid 313 and (nam \ e N or name CA or name C or name O or name CB )) or resid 314 through 321 or (re \ sid 322 and (name N or name CA or name C or name O or name CB )) or resid 323 th \ rough 324 or (resid 325 through 328 and (name N or name CA or name C or name O o \ r name CB )) or resid 329 or (resid 330 through 331 and (name N or name CA or na \ me C or name O or name CB )) or resid 332 or (resid 333 and (name N or name CA o \ r name C or name O or name CB )) or resid 334 through 336 or (resid 337 and (nam \ e N or name CA or name C or name O or name CB )) or resid 338 through 342 or (re \ sid 343 through 345 and (name N or name CA or name C or name O or name CB )) or \ resid 346 or (resid 347 and (name N or name CA or name C or name O or name CB )) \ or resid 348 through 356 or (resid 357 and (name N or name CA or name C or name \ O or name CB )) or resid 358 through 368 or (resid 369 through 370 and (name N \ or name CA or name C or name O or name CB )) or resid 371 through 379 or (resid \ 380 and (name N or name CA or name C or name O or name CB )) or resid 381 throug \ h 388 or (resid 389 and (name N or name CA or name C or name O or name CB )) or \ resid 390 through 403 or resid 405 through 430 or (resid 431 and (name N or name \ CA or name C or name O or name CB )) or resid 432 through 440 or (resid 441 and \ (name N or name CA or name C or name O or name CB )) or resid 442 through 453 o \ r (resid 454 through 455 and (name N or name CA or name C or name O or name CB ) \ ) or resid 456 through 457 or (resid 458 and (name N or name CA or name C or nam \ e O or name CB )) or resid 459 through 484 or (resid 485 and (name N or name CA \ or name C or name O or name CB )) or resid 486 through 488 or (resid 489 and (na \ me N or name CA or name C or name O or name CB )) or resid 490 or (resid 491 and \ (name N or name CA or name C or name O or name CB )) or resid 492 through 503 o \ r (resid 504 through 506 and (name N or name CA or name C or name O or name CB ) \ ) or resid 507 through 530 or (resid 531 and (name N or name CA or name C or nam \ e O or name CB )) or resid 532 through 551 or (resid 552 and (name N or name CA \ or name C or name O or name CB )) or resid 553 through 579 or (resid 599 through \ 601 and (name N or name CA or name C or name O or name CB )) or resid 602 throu \ gh 669 or (resid 670 and (name N or name CA or name C or name O or name CB )) or \ resid 671 through 672 or (resid 673 and (name N or name CA or name C or name O \ or name CB )) or resid 674 through 676 or (resid 677 and (name N or name CA or n \ ame C or name O or name CB )) or resid 678 through 700 or (resid 701 through 704 \ and (name N or name CA or name C or name O or name CB )) or resid 705 through 7 \ 11 or (resid 712 and (name N or name CA or name C or name O or name CB )) or res \ id 713 through 721 or (resid 722 and (name N or name CA or name C or name O or n \ ame CB )) or resid 723 through 724 or (resid 725 and (name N or name CA or name \ C or name O or name CB )) or resid 726 through 741 or (resid 742 through 744 and \ (name N or name CA or name C or name O or name CB )) or resid 745 through 785 o \ r (resid 786 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 87 through 804 or (resid 805 and (name N or name CA or name C or name O or name \ CB )) or resid 806 through 808 or (resid 809 and (name N or name CA or name C or \ name O or name CB )) or resid 810 through 811 or (resid 812 through 814 and (na \ me N or name CA or name C or name O or name CB )) or resid 815 or (resid 816 thr \ ough 817 and (name N or name CA or name C or name O or name CB )) or resid 818 t \ hrough 838 or (resid 839 and (name N or name CA or name C or name O or name CB ) \ ) or resid 840 through 902)) } 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: 1.640 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.050 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.007 0.227 24308 Z= 0.351 Angle : 0.868 18.332 33195 Z= 0.482 Chirality : 0.085 4.409 3894 Planarity : 0.005 0.086 4221 Dihedral : 14.999 88.289 8413 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 17.32 % Favored : 82.58 % Rotamer: Outliers : 0.33 % Allowed : 12.05 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.39 (0.11), residues: 3140 helix: -2.86 (0.12), residues: 1081 sheet: -3.66 (0.23), residues: 319 loop : -4.22 (0.12), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 725 TYR 0.036 0.002 TYR B 731 PHE 0.026 0.002 PHE D 683 TRP 0.026 0.002 TRP B 373 HIS 0.009 0.002 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00725 (24284) covalent geometry : angle 0.85689 (33151) SS BOND : bond 0.00728 ( 13) SS BOND : angle 2.00242 ( 26) hydrogen bonds : bond 0.18398 ( 830) hydrogen bonds : angle 7.63219 ( 2385) Misc. bond : bond 0.00261 ( 5) link_BETA1-4 : bond 0.06499 ( 1) link_BETA1-4 : angle 11.37745 ( 3) link_NAG-ASN : bond 0.00630 ( 5) link_NAG-ASN : angle 3.55716 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 301 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8343 (ttm) cc_final: 0.8089 (tpp) REVERT: A 598 LEU cc_start: 0.8132 (mt) cc_final: 0.7887 (mt) REVERT: A 834 MET cc_start: 0.8116 (mmm) cc_final: 0.7870 (mmt) REVERT: B 157 MET cc_start: 0.8961 (ptp) cc_final: 0.8618 (ptm) REVERT: B 307 MET cc_start: 0.6697 (tpt) cc_final: 0.6346 (tmm) REVERT: B 497 MET cc_start: 0.7849 (tpt) cc_final: 0.7512 (tpt) REVERT: C 144 TYR cc_start: 0.6959 (m-80) cc_final: 0.6719 (m-10) REVERT: C 347 MET cc_start: 0.8668 (ttp) cc_final: 0.8365 (tpp) REVERT: C 375 MET cc_start: 0.6731 (mmm) cc_final: 0.6403 (mmt) REVERT: D 386 MET cc_start: 0.8761 (mmm) cc_final: 0.8079 (mmp) REVERT: D 470 LYS cc_start: 0.9363 (ttpt) cc_final: 0.9147 (tppt) outliers start: 8 outliers final: 7 residues processed: 309 average time/residue: 0.1369 time to fit residues: 70.1741 Evaluate side-chains 236 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 229 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 0.0670 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 134 HIS ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS A 177 GLN A 291 GLN A 294 ASN A 498 HIS A 513 ASN A 542 ASN A 824 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN B 803 ASN B 840 HIS C 162 HIS C 425 HIS C 498 HIS C 508 GLN C 546 GLN C 580 GLN C 730 HIS C 731 ASN D 118 GLN D 153 GLN D 323 ASN D 775 GLN D 802 HIS D 817 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.089642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074629 restraints weight = 99272.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.076128 restraints weight = 61970.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.076700 restraints weight = 42523.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.076900 restraints weight = 36172.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.077022 restraints weight = 34079.185| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24308 Z= 0.160 Angle : 0.737 11.592 33195 Z= 0.381 Chirality : 0.047 0.211 3894 Planarity : 0.005 0.083 4221 Dihedral : 7.432 80.777 3508 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.13), residues: 3140 helix: -1.35 (0.14), residues: 1111 sheet: -3.32 (0.24), residues: 328 loop : -3.49 (0.13), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 815 TYR 0.020 0.001 TYR C 114 PHE 0.025 0.002 PHE D 671 TRP 0.016 0.002 TRP D 285 HIS 0.009 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00349 (24284) covalent geometry : angle 0.72911 (33151) SS BOND : bond 0.00792 ( 13) SS BOND : angle 2.39082 ( 26) hydrogen bonds : bond 0.05332 ( 830) hydrogen bonds : angle 5.87431 ( 2385) Misc. bond : bond 0.00382 ( 5) link_BETA1-4 : bond 0.00192 ( 1) link_BETA1-4 : angle 3.94589 ( 3) link_NAG-ASN : bond 0.00701 ( 5) link_NAG-ASN : angle 3.59213 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.7619 (mpp) cc_final: 0.7208 (mpp) REVERT: A 523 MET cc_start: 0.8431 (tpp) cc_final: 0.8187 (tpt) REVERT: A 723 MET cc_start: 0.6508 (mtm) cc_final: 0.6137 (mtt) REVERT: A 834 MET cc_start: 0.8373 (mmm) cc_final: 0.8162 (mmt) REVERT: B 142 MET cc_start: 0.7787 (mmm) cc_final: 0.7310 (mmt) REVERT: B 497 MET cc_start: 0.7754 (tpt) cc_final: 0.7479 (tpp) REVERT: B 609 LEU cc_start: 0.8985 (mp) cc_final: 0.8766 (mp) REVERT: B 662 GLN cc_start: 0.8715 (pm20) cc_final: 0.8148 (tm-30) REVERT: B 695 ILE cc_start: 0.8861 (mt) cc_final: 0.8591 (tp) REVERT: B 739 MET cc_start: 0.9124 (mmm) cc_final: 0.8825 (mmt) REVERT: C 42 PHE cc_start: 0.8434 (m-80) cc_final: 0.8118 (m-80) REVERT: C 125 MET cc_start: 0.7890 (mpp) cc_final: 0.7078 (mpp) REVERT: C 144 TYR cc_start: 0.6738 (m-80) cc_final: 0.6439 (m-10) REVERT: C 347 MET cc_start: 0.8770 (ttp) cc_final: 0.8338 (tpp) REVERT: C 508 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8491 (pp30) REVERT: C 715 ARG cc_start: 0.7864 (ttm110) cc_final: 0.7602 (tpt90) REVERT: C 790 LYS cc_start: 0.9074 (tmtt) cc_final: 0.8765 (tptp) REVERT: D 134 MET cc_start: 0.7898 (mmm) cc_final: 0.7299 (mmt) REVERT: D 161 MET cc_start: 0.8424 (mtm) cc_final: 0.8198 (ttm) REVERT: D 386 MET cc_start: 0.8875 (mmm) cc_final: 0.8394 (mmp) REVERT: D 470 LYS cc_start: 0.9403 (ttpt) cc_final: 0.9160 (tppt) REVERT: D 815 ILE cc_start: 0.9347 (pt) cc_final: 0.9069 (mt) REVERT: D 824 MET cc_start: 0.7349 (mmt) cc_final: 0.6950 (mmt) outliers start: 2 outliers final: 0 residues processed: 328 average time/residue: 0.1356 time to fit residues: 74.6216 Evaluate side-chains 236 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 130 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 313 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 171 optimal weight: 0.0010 chunk 189 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 425 HIS A 426 GLN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 672 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.091485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.076070 restraints weight = 98576.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.077488 restraints weight = 62046.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.078368 restraints weight = 41086.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.078617 restraints weight = 34399.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.078742 restraints weight = 32656.083| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24308 Z= 0.130 Angle : 0.685 11.477 33195 Z= 0.351 Chirality : 0.045 0.205 3894 Planarity : 0.005 0.082 4221 Dihedral : 7.001 84.269 3508 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.14), residues: 3140 helix: -0.76 (0.15), residues: 1130 sheet: -2.95 (0.25), residues: 324 loop : -3.20 (0.13), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 418 TYR 0.019 0.001 TYR C 816 PHE 0.020 0.001 PHE D 671 TRP 0.033 0.001 TRP A 160 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00285 (24284) covalent geometry : angle 0.67995 (33151) SS BOND : bond 0.00662 ( 13) SS BOND : angle 1.84036 ( 26) hydrogen bonds : bond 0.04737 ( 830) hydrogen bonds : angle 5.44626 ( 2385) Misc. bond : bond 0.00444 ( 5) link_BETA1-4 : bond 0.00825 ( 1) link_BETA1-4 : angle 2.78181 ( 3) link_NAG-ASN : bond 0.00363 ( 5) link_NAG-ASN : angle 3.06704 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 MET cc_start: 0.6652 (mtm) cc_final: 0.6401 (mtt) REVERT: B 157 MET cc_start: 0.8996 (ptp) cc_final: 0.8565 (ptp) REVERT: B 194 PHE cc_start: 0.8479 (m-80) cc_final: 0.7774 (m-80) REVERT: B 497 MET cc_start: 0.7659 (tpt) cc_final: 0.7340 (tpt) REVERT: B 662 GLN cc_start: 0.8585 (pm20) cc_final: 0.8213 (tm-30) REVERT: B 695 ILE cc_start: 0.8801 (mt) cc_final: 0.8518 (tp) REVERT: B 739 MET cc_start: 0.8988 (mmm) cc_final: 0.8773 (mmt) REVERT: C 42 PHE cc_start: 0.8300 (m-80) cc_final: 0.8002 (m-80) REVERT: C 125 MET cc_start: 0.8053 (mpp) cc_final: 0.7209 (mpp) REVERT: C 347 MET cc_start: 0.8731 (ttp) cc_final: 0.7500 (tmm) REVERT: C 522 MET cc_start: 0.8660 (pmm) cc_final: 0.8216 (pmm) REVERT: C 790 LYS cc_start: 0.9087 (tmtt) cc_final: 0.8770 (tptp) REVERT: C 839 MET cc_start: 0.8638 (mtp) cc_final: 0.8302 (mtm) REVERT: D 134 MET cc_start: 0.7887 (mmm) cc_final: 0.7084 (mmt) REVERT: D 386 MET cc_start: 0.8699 (mmm) cc_final: 0.8090 (mmp) REVERT: D 431 ARG cc_start: 0.8420 (ttm110) cc_final: 0.7970 (tpm170) REVERT: D 432 ASN cc_start: 0.8321 (p0) cc_final: 0.7403 (p0) REVERT: D 470 LYS cc_start: 0.9394 (ttpt) cc_final: 0.9116 (tppt) REVERT: D 809 MET cc_start: 0.8184 (tmm) cc_final: 0.7981 (tmm) REVERT: D 815 ILE cc_start: 0.9343 (pt) cc_final: 0.9059 (mt) REVERT: D 824 MET cc_start: 0.7329 (mmt) cc_final: 0.6959 (mmt) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1342 time to fit residues: 74.2621 Evaluate side-chains 241 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 153 optimal weight: 6.9990 chunk 263 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN C 730 HIS ** C 801 HIS ** 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 = 0.3662 r_free = 0.3662 target = 0.089691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.074245 restraints weight = 98585.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.076144 restraints weight = 59380.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.076680 restraints weight = 43498.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.076809 restraints weight = 36104.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.077420 restraints weight = 33796.609| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24308 Z= 0.198 Angle : 0.718 13.943 33195 Z= 0.369 Chirality : 0.046 0.197 3894 Planarity : 0.005 0.083 4221 Dihedral : 7.036 84.217 3508 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.14), residues: 3140 helix: -0.73 (0.15), residues: 1137 sheet: -2.89 (0.26), residues: 314 loop : -3.09 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 544 TYR 0.033 0.002 TYR A 253 PHE 0.019 0.002 PHE D 563 TRP 0.031 0.002 TRP A 160 HIS 0.007 0.001 HIS C 801 Details of bonding type rmsd covalent geometry : bond 0.00439 (24284) covalent geometry : angle 0.71231 (33151) SS BOND : bond 0.00616 ( 13) SS BOND : angle 2.18966 ( 26) hydrogen bonds : bond 0.04813 ( 830) hydrogen bonds : angle 5.50932 ( 2385) Misc. bond : bond 0.00273 ( 5) link_BETA1-4 : bond 0.00570 ( 1) link_BETA1-4 : angle 2.72851 ( 3) link_NAG-ASN : bond 0.00398 ( 5) link_NAG-ASN : angle 2.90252 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.7589 (mpp) cc_final: 0.7151 (mpp) REVERT: A 522 MET cc_start: 0.8103 (ptt) cc_final: 0.7845 (ptp) REVERT: A 723 MET cc_start: 0.6554 (mtm) cc_final: 0.6049 (mtt) REVERT: B 157 MET cc_start: 0.9023 (ptp) cc_final: 0.8561 (ptm) REVERT: B 194 PHE cc_start: 0.8563 (m-80) cc_final: 0.7861 (m-80) REVERT: B 497 MET cc_start: 0.7672 (tpt) cc_final: 0.7350 (tpt) REVERT: B 695 ILE cc_start: 0.8956 (mt) cc_final: 0.8648 (tp) REVERT: C 42 PHE cc_start: 0.8418 (m-80) cc_final: 0.8066 (m-80) REVERT: C 125 MET cc_start: 0.8139 (mpp) cc_final: 0.7908 (mpp) REVERT: C 347 MET cc_start: 0.8716 (ttp) cc_final: 0.7462 (tmm) REVERT: C 727 MET cc_start: 0.8015 (mtt) cc_final: 0.7638 (mmm) REVERT: C 790 LYS cc_start: 0.9138 (tmtt) cc_final: 0.8917 (tptp) REVERT: C 795 LEU cc_start: 0.9037 (tp) cc_final: 0.8801 (pp) REVERT: C 839 MET cc_start: 0.8670 (mtp) cc_final: 0.8364 (mtm) REVERT: D 386 MET cc_start: 0.8753 (mmm) cc_final: 0.8088 (mmp) REVERT: D 470 LYS cc_start: 0.9425 (ttpt) cc_final: 0.9142 (tppt) REVERT: D 563 PHE cc_start: 0.8633 (m-80) cc_final: 0.8103 (m-80) REVERT: D 824 MET cc_start: 0.7361 (mmt) cc_final: 0.7016 (mmt) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1278 time to fit residues: 65.6716 Evaluate side-chains 229 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 243 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 310 optimal weight: 0.9990 chunk 275 optimal weight: 0.0870 chunk 133 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 165 optimal weight: 0.0870 chunk 92 optimal weight: 7.9990 chunk 249 optimal weight: 8.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 637 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.093223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.077598 restraints weight = 93920.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.079378 restraints weight = 56233.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.080234 restraints weight = 37021.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.080814 restraints weight = 32054.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.080948 restraints weight = 28374.284| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24308 Z= 0.117 Angle : 0.662 12.361 33195 Z= 0.337 Chirality : 0.045 0.196 3894 Planarity : 0.005 0.083 4221 Dihedral : 6.648 84.820 3508 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.14), residues: 3140 helix: -0.31 (0.15), residues: 1141 sheet: -2.60 (0.26), residues: 308 loop : -2.90 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 124 TYR 0.025 0.001 TYR C 816 PHE 0.026 0.001 PHE B 577 TRP 0.035 0.001 TRP A 160 HIS 0.005 0.001 HIS D 486 Details of bonding type rmsd covalent geometry : bond 0.00248 (24284) covalent geometry : angle 0.65762 (33151) SS BOND : bond 0.00465 ( 13) SS BOND : angle 1.62702 ( 26) hydrogen bonds : bond 0.04179 ( 830) hydrogen bonds : angle 5.05177 ( 2385) Misc. bond : bond 0.00252 ( 5) link_BETA1-4 : bond 0.01148 ( 1) link_BETA1-4 : angle 2.94432 ( 3) link_NAG-ASN : bond 0.00294 ( 5) link_NAG-ASN : angle 2.77040 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 MET cc_start: 0.8266 (ttm) cc_final: 0.8059 (ttt) REVERT: A 655 MET cc_start: 0.9022 (tpp) cc_final: 0.8554 (mmm) REVERT: A 723 MET cc_start: 0.6382 (mtm) cc_final: 0.5832 (mtt) REVERT: A 783 MET cc_start: 0.7361 (mpp) cc_final: 0.6876 (mpp) REVERT: B 194 PHE cc_start: 0.8563 (m-80) cc_final: 0.7857 (m-80) REVERT: B 497 MET cc_start: 0.7788 (tpt) cc_final: 0.7477 (tpt) REVERT: B 695 ILE cc_start: 0.8935 (mt) cc_final: 0.8663 (tp) REVERT: C 42 PHE cc_start: 0.8282 (m-80) cc_final: 0.7923 (m-80) REVERT: C 347 MET cc_start: 0.8878 (ttp) cc_final: 0.7584 (tmm) REVERT: C 725 ARG cc_start: 0.8391 (ppt170) cc_final: 0.8110 (ttp-110) REVERT: C 790 LYS cc_start: 0.9182 (tmtt) cc_final: 0.8779 (tptp) REVERT: C 795 LEU cc_start: 0.9074 (tp) cc_final: 0.8694 (pp) REVERT: C 839 MET cc_start: 0.8458 (mtp) cc_final: 0.8152 (mtm) REVERT: D 386 MET cc_start: 0.8415 (mmm) cc_final: 0.7873 (mmp) REVERT: D 431 ARG cc_start: 0.8454 (ttm110) cc_final: 0.8197 (tpm170) REVERT: D 470 LYS cc_start: 0.9478 (ttpt) cc_final: 0.9148 (tppt) REVERT: D 562 MET cc_start: 0.9024 (tmm) cc_final: 0.8748 (tmm) REVERT: D 563 PHE cc_start: 0.8661 (m-80) cc_final: 0.8113 (m-80) REVERT: D 824 MET cc_start: 0.7334 (mmt) cc_final: 0.7028 (mmt) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.1342 time to fit residues: 75.8169 Evaluate side-chains 243 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 127 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 272 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 158 optimal weight: 30.0000 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 174 optimal weight: 20.0000 chunk 258 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 817 GLN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.091698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.076973 restraints weight = 97617.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.077430 restraints weight = 67194.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078376 restraints weight = 50731.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.078536 restraints weight = 42249.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.078779 restraints weight = 37509.517| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24308 Z= 0.167 Angle : 0.689 14.101 33195 Z= 0.351 Chirality : 0.045 0.207 3894 Planarity : 0.005 0.097 4221 Dihedral : 6.646 85.535 3508 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 0.08 % Allowed : 2.36 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.14), residues: 3140 helix: -0.30 (0.15), residues: 1152 sheet: -2.56 (0.26), residues: 324 loop : -2.87 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 139 TYR 0.033 0.001 TYR C 144 PHE 0.019 0.002 PHE D 671 TRP 0.035 0.001 TRP A 160 HIS 0.005 0.001 HIS D 486 Details of bonding type rmsd covalent geometry : bond 0.00377 (24284) covalent geometry : angle 0.68373 (33151) SS BOND : bond 0.00430 ( 13) SS BOND : angle 2.16331 ( 26) hydrogen bonds : bond 0.04326 ( 830) hydrogen bonds : angle 5.13697 ( 2385) Misc. bond : bond 0.00242 ( 5) link_BETA1-4 : bond 0.00833 ( 1) link_BETA1-4 : angle 2.53325 ( 3) link_NAG-ASN : bond 0.00290 ( 5) link_NAG-ASN : angle 2.57925 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 309 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 GLN cc_start: 0.7169 (mp10) cc_final: 0.6930 (mp10) REVERT: A 415 MET cc_start: 0.8251 (ttm) cc_final: 0.8049 (ttt) REVERT: A 655 MET cc_start: 0.8984 (tpp) cc_final: 0.8439 (mmm) REVERT: A 723 MET cc_start: 0.6318 (mtm) cc_final: 0.5785 (mtt) REVERT: A 783 MET cc_start: 0.7368 (mpp) cc_final: 0.6951 (mpp) REVERT: B 194 PHE cc_start: 0.8686 (m-80) cc_final: 0.7981 (m-80) REVERT: B 497 MET cc_start: 0.7811 (tpt) cc_final: 0.7531 (tpt) REVERT: B 544 THR cc_start: 0.7954 (p) cc_final: 0.7714 (p) REVERT: B 695 ILE cc_start: 0.8986 (mt) cc_final: 0.8664 (tp) REVERT: B 824 MET cc_start: 0.4798 (mmt) cc_final: 0.3747 (mmt) REVERT: C 42 PHE cc_start: 0.8426 (m-80) cc_final: 0.8043 (m-80) REVERT: C 165 LEU cc_start: 0.9362 (tp) cc_final: 0.9101 (tt) REVERT: C 347 MET cc_start: 0.8909 (ttp) cc_final: 0.7524 (tmm) REVERT: C 637 ASN cc_start: 0.8115 (t0) cc_final: 0.7886 (t0) REVERT: C 725 ARG cc_start: 0.8434 (ppt170) cc_final: 0.8139 (ttp-110) REVERT: C 790 LYS cc_start: 0.9208 (tmtt) cc_final: 0.8871 (tptp) REVERT: C 795 LEU cc_start: 0.9064 (tp) cc_final: 0.8836 (pp) REVERT: C 839 MET cc_start: 0.8607 (mtp) cc_final: 0.8297 (mtm) REVERT: D 386 MET cc_start: 0.8483 (mmm) cc_final: 0.7846 (mmp) REVERT: D 431 ARG cc_start: 0.8560 (ttm110) cc_final: 0.7986 (tpp-160) REVERT: D 432 ASN cc_start: 0.8407 (p0) cc_final: 0.7924 (p0) REVERT: D 470 LYS cc_start: 0.9404 (ttpt) cc_final: 0.9137 (tppt) REVERT: D 563 PHE cc_start: 0.8626 (m-80) cc_final: 0.8086 (m-80) REVERT: D 824 MET cc_start: 0.7342 (mmt) cc_final: 0.7012 (mmt) outliers start: 2 outliers final: 1 residues processed: 310 average time/residue: 0.1378 time to fit residues: 72.2659 Evaluate side-chains 240 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 119 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 3 optimal weight: 30.0000 chunk 82 optimal weight: 50.0000 chunk 24 optimal weight: 6.9990 chunk 291 optimal weight: 20.0000 chunk 165 optimal weight: 0.0030 chunk 246 optimal weight: 20.0000 chunk 312 optimal weight: 9.9990 overall best weight: 1.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN B 806 ASN C 392 HIS ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS D 817 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.093129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.077952 restraints weight = 96097.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.078886 restraints weight = 66160.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.079780 restraints weight = 46583.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.080289 restraints weight = 38277.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.080534 restraints weight = 34498.351| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24308 Z= 0.124 Angle : 0.659 13.412 33195 Z= 0.335 Chirality : 0.044 0.230 3894 Planarity : 0.005 0.083 4221 Dihedral : 6.467 85.763 3508 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.04 % Allowed : 1.53 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.14), residues: 3140 helix: -0.17 (0.15), residues: 1156 sheet: -2.41 (0.26), residues: 323 loop : -2.78 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 540 TYR 0.024 0.001 TYR C 114 PHE 0.013 0.001 PHE C 218 TRP 0.034 0.001 TRP A 160 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00277 (24284) covalent geometry : angle 0.65365 (33151) SS BOND : bond 0.00397 ( 13) SS BOND : angle 2.14833 ( 26) hydrogen bonds : bond 0.04056 ( 830) hydrogen bonds : angle 4.97040 ( 2385) Misc. bond : bond 0.00246 ( 5) link_BETA1-4 : bond 0.00866 ( 1) link_BETA1-4 : angle 2.77272 ( 3) link_NAG-ASN : bond 0.00228 ( 5) link_NAG-ASN : angle 2.60212 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 GLN cc_start: 0.7089 (mp10) cc_final: 0.6826 (mp10) REVERT: A 723 MET cc_start: 0.6372 (mtm) cc_final: 0.5854 (mtt) REVERT: B 194 PHE cc_start: 0.8633 (m-80) cc_final: 0.7992 (m-80) REVERT: B 497 MET cc_start: 0.7428 (tpt) cc_final: 0.7121 (tpt) REVERT: B 695 ILE cc_start: 0.8913 (mt) cc_final: 0.8618 (tp) REVERT: C 42 PHE cc_start: 0.8385 (m-80) cc_final: 0.8050 (m-80) REVERT: C 347 MET cc_start: 0.8861 (ttp) cc_final: 0.7575 (tmm) REVERT: C 375 MET cc_start: 0.7180 (mmt) cc_final: 0.6798 (tmm) REVERT: C 522 MET cc_start: 0.8831 (pmm) cc_final: 0.8507 (pmm) REVERT: C 637 ASN cc_start: 0.8197 (t0) cc_final: 0.7995 (t0) REVERT: C 725 ARG cc_start: 0.8432 (ppt170) cc_final: 0.8080 (ttp-110) REVERT: C 790 LYS cc_start: 0.9161 (tmtt) cc_final: 0.8783 (tptp) REVERT: C 839 MET cc_start: 0.8489 (mtp) cc_final: 0.8180 (mtm) REVERT: D 386 MET cc_start: 0.8304 (mmm) cc_final: 0.7726 (mmp) REVERT: D 470 LYS cc_start: 0.9399 (ttpt) cc_final: 0.9126 (tppt) REVERT: D 563 PHE cc_start: 0.8645 (m-80) cc_final: 0.8115 (m-80) REVERT: D 824 MET cc_start: 0.7164 (mmt) cc_final: 0.6851 (mmt) outliers start: 1 outliers final: 0 residues processed: 312 average time/residue: 0.1374 time to fit residues: 72.8321 Evaluate side-chains 250 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 112 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 271 optimal weight: 7.9990 chunk 277 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 241 optimal weight: 8.9990 chunk 203 optimal weight: 0.0670 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS B 153 GLN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.093872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.078667 restraints weight = 95390.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.079829 restraints weight = 65249.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.080602 restraints weight = 45768.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.081067 restraints weight = 38553.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.081310 restraints weight = 34880.014| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24308 Z= 0.119 Angle : 0.650 13.125 33195 Z= 0.330 Chirality : 0.044 0.224 3894 Planarity : 0.005 0.083 4221 Dihedral : 6.319 86.376 3508 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.15), residues: 3140 helix: -0.11 (0.15), residues: 1158 sheet: -2.28 (0.26), residues: 322 loop : -2.71 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 115 TYR 0.025 0.001 TYR C 114 PHE 0.017 0.001 PHE A 838 TRP 0.035 0.001 TRP A 160 HIS 0.006 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00263 (24284) covalent geometry : angle 0.64616 (33151) SS BOND : bond 0.00541 ( 13) SS BOND : angle 1.89841 ( 26) hydrogen bonds : bond 0.04005 ( 830) hydrogen bonds : angle 4.89208 ( 2385) Misc. bond : bond 0.00244 ( 5) link_BETA1-4 : bond 0.00733 ( 1) link_BETA1-4 : angle 2.74454 ( 3) link_NAG-ASN : bond 0.00198 ( 5) link_NAG-ASN : angle 2.39510 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.884 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 522 MET cc_start: 0.7817 (ptt) cc_final: 0.7603 (ptt) REVERT: A 723 MET cc_start: 0.6438 (mtm) cc_final: 0.5795 (mtt) REVERT: A 834 MET cc_start: 0.8512 (mmp) cc_final: 0.8020 (mmt) REVERT: B 194 PHE cc_start: 0.8551 (m-80) cc_final: 0.7976 (m-80) REVERT: B 537 MET cc_start: 0.7658 (tpt) cc_final: 0.7012 (tpt) REVERT: B 695 ILE cc_start: 0.8894 (mt) cc_final: 0.8606 (tp) REVERT: B 739 MET cc_start: 0.8933 (mmm) cc_final: 0.8703 (mmt) REVERT: C 42 PHE cc_start: 0.8323 (m-80) cc_final: 0.8064 (m-80) REVERT: C 347 MET cc_start: 0.8851 (ttp) cc_final: 0.7567 (tmm) REVERT: C 375 MET cc_start: 0.7147 (mmt) cc_final: 0.6802 (tmm) REVERT: C 725 ARG cc_start: 0.8380 (ppt170) cc_final: 0.8076 (ttp-110) REVERT: C 795 LEU cc_start: 0.8979 (tp) cc_final: 0.8771 (pp) REVERT: C 839 MET cc_start: 0.8621 (mtp) cc_final: 0.8313 (mtm) REVERT: D 386 MET cc_start: 0.8274 (mmm) cc_final: 0.7705 (mmp) REVERT: D 470 LYS cc_start: 0.9391 (ttpt) cc_final: 0.9143 (tppt) REVERT: D 824 MET cc_start: 0.7161 (mmt) cc_final: 0.6841 (mmt) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.1297 time to fit residues: 69.9132 Evaluate side-chains 250 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 4 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 241 optimal weight: 0.0000 chunk 294 optimal weight: 0.0670 chunk 218 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 637 ASN ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.095236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.079988 restraints weight = 95050.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.081574 restraints weight = 56818.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.081917 restraints weight = 41231.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.082179 restraints weight = 36793.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.082474 restraints weight = 33015.235| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 24308 Z= 0.113 Angle : 0.660 12.492 33195 Z= 0.331 Chirality : 0.044 0.225 3894 Planarity : 0.005 0.082 4221 Dihedral : 6.116 86.609 3508 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.08 % Allowed : 0.66 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.15), residues: 3140 helix: 0.01 (0.15), residues: 1151 sheet: -2.12 (0.26), residues: 345 loop : -2.61 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 233 TYR 0.026 0.001 TYR C 114 PHE 0.031 0.001 PHE B 577 TRP 0.035 0.001 TRP A 160 HIS 0.004 0.001 HIS B 486 Details of bonding type rmsd covalent geometry : bond 0.00248 (24284) covalent geometry : angle 0.65410 (33151) SS BOND : bond 0.00833 ( 13) SS BOND : angle 2.62456 ( 26) hydrogen bonds : bond 0.03758 ( 830) hydrogen bonds : angle 4.78550 ( 2385) Misc. bond : bond 0.00239 ( 5) link_BETA1-4 : bond 0.00787 ( 1) link_BETA1-4 : angle 2.82400 ( 3) link_NAG-ASN : bond 0.00207 ( 5) link_NAG-ASN : angle 2.23857 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 335 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.7903 (ptt) cc_final: 0.7620 (ptt) REVERT: A 655 MET cc_start: 0.8921 (tpp) cc_final: 0.8312 (mmm) REVERT: A 723 MET cc_start: 0.6395 (mtm) cc_final: 0.5728 (mtt) REVERT: A 783 MET cc_start: 0.8061 (mpp) cc_final: 0.7830 (mpp) REVERT: A 834 MET cc_start: 0.8636 (mmp) cc_final: 0.8150 (mmt) REVERT: B 169 PHE cc_start: 0.6341 (m-10) cc_final: 0.5927 (m-10) REVERT: B 497 MET cc_start: 0.7757 (tpt) cc_final: 0.7202 (tpt) REVERT: B 498 ILE cc_start: 0.8435 (mm) cc_final: 0.8042 (mm) REVERT: B 537 MET cc_start: 0.7509 (tpt) cc_final: 0.6912 (tpt) REVERT: B 695 ILE cc_start: 0.8895 (mt) cc_final: 0.8616 (tp) REVERT: C 42 PHE cc_start: 0.8194 (m-80) cc_final: 0.7970 (m-80) REVERT: C 164 ILE cc_start: 0.8574 (mm) cc_final: 0.8298 (mm) REVERT: C 347 MET cc_start: 0.8877 (ttp) cc_final: 0.7600 (tmm) REVERT: C 375 MET cc_start: 0.7338 (mmt) cc_final: 0.6823 (tmm) REVERT: C 795 LEU cc_start: 0.8986 (tp) cc_final: 0.8782 (pp) REVERT: C 839 MET cc_start: 0.8565 (mtp) cc_final: 0.8279 (mtm) REVERT: D 386 MET cc_start: 0.8167 (mmm) cc_final: 0.7618 (mmp) REVERT: D 470 LYS cc_start: 0.9398 (ttpt) cc_final: 0.9149 (tppt) REVERT: D 561 MET cc_start: 0.8413 (ppp) cc_final: 0.8111 (ppp) REVERT: D 616 ASN cc_start: 0.7975 (t0) cc_final: 0.7737 (p0) REVERT: D 824 MET cc_start: 0.7205 (mmt) cc_final: 0.6862 (mmt) outliers start: 2 outliers final: 0 residues processed: 336 average time/residue: 0.1310 time to fit residues: 74.7231 Evaluate side-chains 252 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 108 optimal weight: 0.0030 chunk 213 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 254 optimal weight: 5.9990 chunk 300 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 66 optimal weight: 0.0970 chunk 241 optimal weight: 7.9990 overall best weight: 4.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 HIS ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 730 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.092305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.076765 restraints weight = 97509.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.078687 restraints weight = 61752.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.079174 restraints weight = 41032.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.079468 restraints weight = 37267.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.079540 restraints weight = 34009.280| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 24308 Z= 0.185 Angle : 0.710 14.461 33195 Z= 0.359 Chirality : 0.046 0.225 3894 Planarity : 0.005 0.081 4221 Dihedral : 6.331 86.731 3508 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.15), residues: 3140 helix: -0.13 (0.15), residues: 1169 sheet: -2.07 (0.27), residues: 329 loop : -2.68 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 139 TYR 0.033 0.002 TYR B 287 PHE 0.023 0.002 PHE B 784 TRP 0.039 0.002 TRP A 160 HIS 0.012 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00419 (24284) covalent geometry : angle 0.70635 (33151) SS BOND : bond 0.00394 ( 13) SS BOND : angle 1.93857 ( 26) hydrogen bonds : bond 0.04238 ( 830) hydrogen bonds : angle 5.01243 ( 2385) Misc. bond : bond 0.00231 ( 5) link_BETA1-4 : bond 0.00740 ( 1) link_BETA1-4 : angle 2.18902 ( 3) link_NAG-ASN : bond 0.00242 ( 5) link_NAG-ASN : angle 2.37402 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6280 Ramachandran restraints generated. 3140 Oldfield, 0 Emsley, 3140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.8827 (ptm) cc_final: 0.8554 (ptt) REVERT: A 491 MET cc_start: 0.8175 (tpp) cc_final: 0.7959 (tpp) REVERT: A 522 MET cc_start: 0.8048 (ptt) cc_final: 0.7841 (ptt) REVERT: A 723 MET cc_start: 0.6449 (mtm) cc_final: 0.5809 (mtt) REVERT: A 834 MET cc_start: 0.8670 (mmp) cc_final: 0.8167 (mmt) REVERT: B 169 PHE cc_start: 0.6507 (m-10) cc_final: 0.6036 (m-10) REVERT: B 194 PHE cc_start: 0.8573 (m-80) cc_final: 0.7982 (m-80) REVERT: B 497 MET cc_start: 0.7639 (tpt) cc_final: 0.7328 (tpt) REVERT: B 695 ILE cc_start: 0.8875 (mt) cc_final: 0.8603 (tp) REVERT: C 42 PHE cc_start: 0.8406 (m-80) cc_final: 0.8199 (m-80) REVERT: C 165 LEU cc_start: 0.9275 (tp) cc_final: 0.8932 (tt) REVERT: C 347 MET cc_start: 0.8923 (ttp) cc_final: 0.7557 (tmm) REVERT: C 375 MET cc_start: 0.6962 (mmt) cc_final: 0.6659 (tmm) REVERT: C 839 MET cc_start: 0.8659 (mtp) cc_final: 0.8339 (mtm) REVERT: D 386 MET cc_start: 0.8333 (mmm) cc_final: 0.7792 (mmp) REVERT: D 431 ARG cc_start: 0.8401 (ttm110) cc_final: 0.8057 (tpp-160) REVERT: D 432 ASN cc_start: 0.8493 (p0) cc_final: 0.8069 (p0) REVERT: D 470 LYS cc_start: 0.9380 (ttpt) cc_final: 0.9147 (tppt) REVERT: D 561 MET cc_start: 0.8425 (ppp) cc_final: 0.8139 (ppp) REVERT: D 824 MET cc_start: 0.7184 (mmt) cc_final: 0.6798 (mmt) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1327 time to fit residues: 69.0971 Evaluate side-chains 239 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.0270 chunk 287 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 181 optimal weight: 0.0060 chunk 106 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 overall best weight: 0.9856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS B 616 ASN ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.094973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.079905 restraints weight = 94962.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.081230 restraints weight = 57448.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.081812 restraints weight = 41432.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.082052 restraints weight = 37126.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.082248 restraints weight = 33924.204| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24308 Z= 0.116 Angle : 0.671 13.277 33195 Z= 0.336 Chirality : 0.044 0.222 3894 Planarity : 0.005 0.082 4221 Dihedral : 6.094 87.272 3508 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.15), residues: 3140 helix: 0.02 (0.15), residues: 1158 sheet: -1.92 (0.27), residues: 340 loop : -2.54 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 139 TYR 0.032 0.001 TYR B 287 PHE 0.032 0.001 PHE B 577 TRP 0.039 0.001 TRP A 160 HIS 0.012 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00256 (24284) covalent geometry : angle 0.66798 (33151) SS BOND : bond 0.00424 ( 13) SS BOND : angle 1.66891 ( 26) hydrogen bonds : bond 0.03929 ( 830) hydrogen bonds : angle 4.81079 ( 2385) Misc. bond : bond 0.00239 ( 5) link_BETA1-4 : bond 0.00969 ( 1) link_BETA1-4 : angle 2.55802 ( 3) link_NAG-ASN : bond 0.00197 ( 5) link_NAG-ASN : angle 2.31169 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3433.65 seconds wall clock time: 60 minutes 23.20 seconds (3623.20 seconds total)