Starting phenix.real_space_refine on Thu Feb 5 08:31:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jms_61612/02_2026/9jms_61612_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jms_61612/02_2026/9jms_61612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jms_61612/02_2026/9jms_61612_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jms_61612/02_2026/9jms_61612_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jms_61612/02_2026/9jms_61612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jms_61612/02_2026/9jms_61612.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 9923 2.51 5 N 2688 2.21 5 O 2969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15653 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4633 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4637 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 553} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 4645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4645 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 940 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 798 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 2.89, per 1000 atoms: 0.18 Number of scatterers: 15653 At special positions: 0 Unit cell: (89.7, 124.15, 179.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 2969 8.00 N 2688 7.00 C 9923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 584 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 645 " distance=2.04 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 584 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 540 " distance=2.03 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " 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=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 566.2 milliseconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3720 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 44 sheets defined 20.6% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.694A pdb=" N THR A 366 " --> pdb=" O PRO A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 417 through 433 removed outlier: 3.572A pdb=" N GLU A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 554 removed outlier: 3.517A pdb=" N LEU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 567 removed outlier: 3.758A pdb=" N LEU A 561 " --> pdb=" O ASN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 713 through 722 removed outlier: 3.610A pdb=" N ARG A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.665A pdb=" N THR B 366 " --> pdb=" O PRO B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 416 through 433 removed outlier: 4.478A pdb=" N GLU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 431 " --> pdb=" O ASN B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 554 removed outlier: 3.546A pdb=" N HIS B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN B 529 " --> pdb=" O GLN B 525 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 567 removed outlier: 3.606A pdb=" N THR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'B' and resid 713 through 722 Processing helix chain 'B' and resid 723 through 729 Processing helix chain 'C' and resid 199 through 206 removed outlier: 3.509A pdb=" N THR C 204 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 321 through 323 No H-bonds generated for 'chain 'C' and resid 321 through 323' Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 417 through 433 removed outlier: 3.713A pdb=" N ARG C 423 " --> pdb=" O LYS C 419 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 424 " --> pdb=" O GLU C 420 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR C 431 " --> pdb=" O ASN C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 554 removed outlier: 3.612A pdb=" N HIS C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA C 548 " --> pdb=" O ASN C 544 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU C 549 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 567 removed outlier: 3.743A pdb=" N LEU C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 676 No H-bonds generated for 'chain 'C' and resid 674 through 676' Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'C' and resid 713 through 722 removed outlier: 3.529A pdb=" N ARG C 720 " --> pdb=" O GLU C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 729 removed outlier: 3.553A pdb=" N TYR C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.832A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 90 removed outlier: 3.657A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 90' Processing helix chain 'L' and resid 78 through 82 removed outlier: 4.307A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 573 through 574 removed outlier: 6.927A pdb=" N ILE A 130 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE B 679 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG A 132 " --> pdb=" O ILE B 679 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 403 removed outlier: 3.548A pdb=" N PHE A 400 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP A 374 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LYS A 157 " --> pdb=" O TRP A 374 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU A 376 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 155 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLU A 378 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ALA A 153 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLU A 150 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 398 through 403 removed outlier: 3.548A pdb=" N PHE A 400 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP A 374 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LYS A 157 " --> pdb=" O TRP A 374 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU A 376 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 155 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLU A 378 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ALA A 153 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLU A 150 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 197 removed outlier: 5.654A pdb=" N ILE A 188 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP A 180 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 190 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 241 through 242 removed outlier: 3.558A pdb=" N ALA A 167 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 340 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN A 333 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TYR A 331 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA A 346 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU A 329 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN A 348 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN A 327 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 350 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE A 325 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 212 through 214 Processing sheet with id=AA7, first strand: chain 'A' and resid 216 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA9, first strand: chain 'A' and resid 594 through 595 Processing sheet with id=AB1, first strand: chain 'A' and resid 607 through 609 Processing sheet with id=AB2, first strand: chain 'A' and resid 628 through 629 Processing sheet with id=AB3, first strand: chain 'A' and resid 650 through 655 removed outlier: 3.598A pdb=" N ARG A 669 " --> pdb=" O TYR A 661 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLU A 663 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 677 through 679 removed outlier: 6.281A pdb=" N GLY A 677 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 573 through 574 removed outlier: 7.134A pdb=" N ILE B 130 " --> pdb=" O GLY C 677 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE C 679 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG B 132 " --> pdb=" O ILE C 679 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 398 through 403 removed outlier: 7.043A pdb=" N VAL B 155 " --> pdb=" O TRP B 374 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU B 376 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA B 153 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B 378 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY B 151 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 380 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR B 149 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU B 150 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 398 through 403 removed outlier: 7.043A pdb=" N VAL B 155 " --> pdb=" O TRP B 374 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU B 376 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ALA B 153 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B 378 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY B 151 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 380 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR B 149 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU B 150 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 186 through 197 removed outlier: 5.716A pdb=" N ILE B 188 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP B 180 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 190 " --> pdb=" O THR B 178 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 186 through 197 removed outlier: 5.716A pdb=" N ILE B 188 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP B 180 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 190 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LYS B 166 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASN B 360 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA B 345 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 330 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 212 through 213 Processing sheet with id=AC2, first strand: chain 'B' and resid 216 through 221 Processing sheet with id=AC3, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AC4, first strand: chain 'B' and resid 334 through 335 removed outlier: 3.582A pdb=" N ALA B 340 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 594 through 595 Processing sheet with id=AC6, first strand: chain 'B' and resid 607 through 609 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 655 removed outlier: 6.962A pdb=" N TYR B 661 " --> pdb=" O VAL B 668 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 119 through 120 removed outlier: 4.534A pdb=" N PHE C 119 " --> pdb=" O LEU C 587 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 398 through 403 removed outlier: 3.531A pdb=" N PHE C 389 " --> pdb=" O SER C 402 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 155 " --> pdb=" O TRP C 374 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLU C 376 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA C 153 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU C 378 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY C 151 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL C 380 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR C 149 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU C 150 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 398 through 403 removed outlier: 3.531A pdb=" N PHE C 389 " --> pdb=" O SER C 402 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 155 " --> pdb=" O TRP C 374 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLU C 376 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA C 153 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU C 378 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY C 151 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL C 380 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR C 149 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU C 150 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 453 " --> pdb=" O ALA C 449 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 186 through 197 removed outlier: 6.662A pdb=" N THR C 178 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG C 191 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 176 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA C 193 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL C 174 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG C 195 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS C 172 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR C 170 " --> pdb=" O PRO C 197 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 186 through 197 removed outlier: 6.662A pdb=" N THR C 178 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG C 191 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 176 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA C 193 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL C 174 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG C 195 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS C 172 " --> pdb=" O ARG C 195 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR C 170 " --> pdb=" O PRO C 197 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 356 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA C 345 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY C 330 " --> pdb=" O ALA C 345 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 212 through 214 Processing sheet with id=AD5, first strand: chain 'C' and resid 216 through 221 Processing sheet with id=AD6, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AD7, first strand: chain 'C' and resid 334 through 335 Processing sheet with id=AD8, first strand: chain 'C' and resid 594 through 595 Processing sheet with id=AD9, first strand: chain 'C' and resid 607 through 609 Processing sheet with id=AE1, first strand: chain 'C' and resid 628 through 629 Processing sheet with id=AE2, first strand: chain 'C' and resid 650 through 655 removed outlier: 3.805A pdb=" N ARG C 669 " --> pdb=" O TYR C 661 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLU C 663 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TYR C 667 " --> pdb=" O GLU C 663 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.664A pdb=" N GLU H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR H 95 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.664A pdb=" N GLU H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AE7, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.816A pdb=" N LEU L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.423A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1599 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: 2.66 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4901 1.33 - 1.46: 3988 1.46 - 1.58: 7025 1.58 - 1.70: 0 1.70 - 1.83: 112 Bond restraints: 16026 Sorted by residual: bond pdb=" C ASP A 237 " pdb=" N MET A 238 " ideal model delta sigma weight residual 1.331 1.226 0.105 2.07e-02 2.33e+03 2.55e+01 bond pdb=" CA SER A 415 " pdb=" CB SER A 415 " ideal model delta sigma weight residual 1.527 1.482 0.044 1.39e-02 5.18e+03 1.01e+01 bond pdb=" N GLU A 134 " pdb=" CA GLU A 134 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.14e-02 7.69e+03 8.65e+00 bond pdb=" N LEU A 133 " pdb=" CA LEU A 133 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.53e+00 bond pdb=" N GLU B 134 " pdb=" CA GLU B 134 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.29e-02 6.01e+03 7.22e+00 ... (remaining 16021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 20662 1.99 - 3.98: 992 3.98 - 5.96: 106 5.96 - 7.95: 20 7.95 - 9.94: 4 Bond angle restraints: 21784 Sorted by residual: angle pdb=" C SER B 589 " pdb=" N ASP B 590 " pdb=" CA ASP B 590 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" CA THR B 702 " pdb=" C THR B 702 " pdb=" O THR B 702 " ideal model delta sigma weight residual 121.88 117.06 4.82 1.13e+00 7.83e-01 1.82e+01 angle pdb=" N PHE B 554 " pdb=" CA PHE B 554 " pdb=" C PHE B 554 " ideal model delta sigma weight residual 109.81 118.57 -8.76 2.21e+00 2.05e-01 1.57e+01 angle pdb=" N GLN B 416 " pdb=" CA GLN B 416 " pdb=" C GLN B 416 " ideal model delta sigma weight residual 113.72 108.60 5.12 1.30e+00 5.92e-01 1.55e+01 angle pdb=" N PHE C 554 " pdb=" CA PHE C 554 " pdb=" C PHE C 554 " ideal model delta sigma weight residual 109.81 118.50 -8.69 2.21e+00 2.05e-01 1.54e+01 ... (remaining 21779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.66: 9035 14.66 - 29.32: 394 29.32 - 43.98: 106 43.98 - 58.64: 29 58.64 - 73.29: 10 Dihedral angle restraints: 9574 sinusoidal: 3788 harmonic: 5786 Sorted by residual: dihedral pdb=" CD ARG C 310 " pdb=" NE ARG C 310 " pdb=" CZ ARG C 310 " pdb=" NH1 ARG C 310 " ideal model delta sinusoidal sigma weight residual 0.00 63.30 -63.30 1 1.00e+01 1.00e-02 5.29e+01 dihedral pdb=" CB CYS C 369 " pdb=" SG CYS C 369 " pdb=" SG CYS C 417 " pdb=" CB CYS C 417 " ideal model delta sinusoidal sigma weight residual 93.00 154.38 -61.38 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" CA CYS C 417 " pdb=" C CYS C 417 " pdb=" N VAL C 418 " pdb=" CA VAL C 418 " ideal model delta harmonic sigma weight residual -180.00 -150.97 -29.03 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 9571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1338 0.043 - 0.087: 729 0.087 - 0.130: 278 0.130 - 0.174: 61 0.174 - 0.217: 15 Chirality restraints: 2421 Sorted by residual: chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL A 372 " pdb=" CA VAL A 372 " pdb=" CG1 VAL A 372 " pdb=" CG2 VAL A 372 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR H 28 " pdb=" CA THR H 28 " pdb=" OG1 THR H 28 " pdb=" CG2 THR H 28 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2418 not shown) Planarity restraints: 2791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 310 " -0.979 9.50e-02 1.11e+02 4.39e-01 1.17e+02 pdb=" NE ARG C 310 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG C 310 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 310 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 310 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 137 " 0.435 9.50e-02 1.11e+02 1.95e-01 2.33e+01 pdb=" NE ARG B 137 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 137 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 137 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 137 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 137 " -0.350 9.50e-02 1.11e+02 1.57e-01 1.51e+01 pdb=" NE ARG A 137 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 137 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 137 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 137 " -0.012 2.00e-02 2.50e+03 ... (remaining 2788 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3553 2.77 - 3.30: 13425 3.30 - 3.83: 26163 3.83 - 4.37: 29786 4.37 - 4.90: 52990 Nonbonded interactions: 125917 Sorted by model distance: nonbonded pdb=" OD2 ASP B 208 " pdb=" OH TYR B 331 " model vdw 2.237 3.040 nonbonded pdb=" OG SER C 511 " pdb=" OE1 GLU C 513 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR H 103 " pdb=" OH TYR L 95 " model vdw 2.266 3.040 nonbonded pdb=" OD2 ASP A 208 " pdb=" OH TYR A 331 " model vdw 2.271 3.040 nonbonded pdb=" O VAL L 29 " pdb=" OH TYR L 70 " model vdw 2.278 3.040 ... (remaining 125912 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 115 through 599 or (resid 600 and (name N or name CA or na \ me C or name O or name CB )) or resid 601 through 736)) selection = (chain 'B' and ((resid 115 through 116 and (name N or name CA or name C or name \ O or name CB )) or resid 117 through 588 or (resid 589 through 590 and (name N o \ r name CA or name C or name O or name CB )) or resid 591 through 616 or resid 62 \ 5 through 736)) selection = (chain 'C' and ((resid 115 through 116 and (name N or name CA or name C or name \ O or name CB )) or resid 117 through 588 or (resid 589 through 590 and (name N o \ r name CA or name C or name O or name CB )) or resid 591 through 596 or (resid 5 \ 97 and (name N or name CA or name C or name O or name CB )) or resid 598 through \ 599 or (resid 600 and (name N or name CA or name C or name O or name CB )) or r \ esid 601 through 665 or (resid 666 and (name N or name CA or name C or name O or \ name CB )) or resid 667 through 736)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.980 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.105 16043 Z= 0.590 Angle : 0.963 9.940 21818 Z= 0.557 Chirality : 0.060 0.217 2421 Planarity : 0.012 0.439 2791 Dihedral : 9.661 73.295 5803 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % Rotamer: Outliers : 0.93 % Allowed : 1.34 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.16), residues: 1936 helix: -3.83 (0.15), residues: 298 sheet: -2.55 (0.19), residues: 521 loop : -1.69 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 693 TYR 0.065 0.004 TYR B 385 PHE 0.058 0.004 PHE L 61 TRP 0.033 0.003 TRP H 112 HIS 0.020 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.01292 (16026) covalent geometry : angle 0.96197 (21784) SS BOND : bond 0.00392 ( 17) SS BOND : angle 1.41136 ( 34) hydrogen bonds : bond 0.24878 ( 546) hydrogen bonds : angle 10.14666 ( 1599) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 367 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.7289 (m110) cc_final: 0.6240 (m-40) REVERT: A 148 PHE cc_start: 0.7613 (p90) cc_final: 0.7282 (p90) REVERT: A 233 LYS cc_start: 0.6371 (mttt) cc_final: 0.5644 (mtmt) REVERT: A 238 MET cc_start: 0.7459 (mtp) cc_final: 0.7131 (mtm) REVERT: A 339 ARG cc_start: 0.7744 (mtt-85) cc_final: 0.6984 (mtt90) REVERT: A 365 ARG cc_start: 0.7246 (ttp-110) cc_final: 0.6319 (mmt180) REVERT: A 390 ARG cc_start: 0.5580 (mtt-85) cc_final: 0.4925 (mtm180) REVERT: A 403 GLU cc_start: 0.6162 (pm20) cc_final: 0.5727 (mt-10) REVERT: A 416 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6553 (pp30) REVERT: A 433 ARG cc_start: 0.7345 (ttt180) cc_final: 0.7064 (ttm170) REVERT: A 522 ASP cc_start: 0.7301 (m-30) cc_final: 0.6875 (m-30) REVERT: A 530 GLU cc_start: 0.7070 (tp30) cc_final: 0.6848 (tp30) REVERT: A 551 SER cc_start: 0.7869 (t) cc_final: 0.7625 (p) REVERT: A 634 GLU cc_start: 0.7490 (tt0) cc_final: 0.7163 (mt-10) REVERT: A 649 HIS cc_start: 0.6828 (t-90) cc_final: 0.6257 (t-170) REVERT: A 665 TYR cc_start: 0.6613 (m-80) cc_final: 0.6020 (m-80) REVERT: A 688 THR cc_start: 0.7478 (m) cc_final: 0.7192 (p) REVERT: A 691 LYS cc_start: 0.7820 (mmpt) cc_final: 0.7590 (mmtm) REVERT: B 142 TYR cc_start: 0.7076 (m-80) cc_final: 0.6835 (m-80) REVERT: B 166 LYS cc_start: 0.8127 (ptmm) cc_final: 0.7697 (ptpp) REVERT: B 188 ILE cc_start: 0.7873 (mt) cc_final: 0.7541 (tt) REVERT: B 234 ASN cc_start: 0.8519 (m-40) cc_final: 0.8246 (m-40) REVERT: B 258 ASP cc_start: 0.7454 (m-30) cc_final: 0.7085 (m-30) REVERT: B 365 ARG cc_start: 0.8134 (ptt-90) cc_final: 0.7899 (ptt90) REVERT: B 546 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7432 (mm-30) REVERT: B 649 HIS cc_start: 0.6329 (t-90) cc_final: 0.6084 (t-90) REVERT: B 692 ASP cc_start: 0.7835 (m-30) cc_final: 0.7496 (m-30) REVERT: B 694 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7867 (mt-10) REVERT: B 733 LYS cc_start: 0.7876 (ptmm) cc_final: 0.7653 (pttt) REVERT: C 146 LYS cc_start: 0.7333 (mttm) cc_final: 0.6654 (mtpp) REVERT: C 166 LYS cc_start: 0.8306 (ptmm) cc_final: 0.8021 (ptmm) REVERT: C 236 GLN cc_start: 0.6053 (mt0) cc_final: 0.5531 (pt0) REVERT: C 314 TYR cc_start: 0.7147 (p90) cc_final: 0.6901 (p90) REVERT: C 378 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6413 (mp0) REVERT: C 390 ARG cc_start: 0.4970 (mtt-85) cc_final: 0.4652 (mtm110) REVERT: C 403 GLU cc_start: 0.6525 (pm20) cc_final: 0.5840 (pt0) REVERT: C 419 LYS cc_start: 0.6847 (mppt) cc_final: 0.6375 (mmmm) REVERT: C 420 GLU cc_start: 0.7760 (tp30) cc_final: 0.7289 (tm-30) REVERT: C 433 ARG cc_start: 0.7489 (ttt180) cc_final: 0.7206 (mtp180) REVERT: C 435 ASN cc_start: 0.5650 (t0) cc_final: 0.4515 (p0) REVERT: C 635 LEU cc_start: 0.7334 (mt) cc_final: 0.7099 (mm) REVERT: C 694 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7534 (mp0) REVERT: C 716 GLU cc_start: 0.7104 (tp30) cc_final: 0.6509 (tp30) REVERT: C 721 ASN cc_start: 0.7213 (m-40) cc_final: 0.7000 (t0) REVERT: H 10 GLU cc_start: 0.6636 (tp30) cc_final: 0.6275 (mp0) REVERT: H 77 TYR cc_start: 0.5408 (m-80) cc_final: 0.5208 (m-10) REVERT: L 20 THR cc_start: 0.7389 (t) cc_final: 0.7149 (m) REVERT: L 21 MET cc_start: 0.5908 (mtt) cc_final: 0.5592 (mtt) REVERT: L 52 ASN cc_start: 0.6302 (m-40) cc_final: 0.6055 (m-40) outliers start: 16 outliers final: 5 residues processed: 379 average time/residue: 0.1387 time to fit residues: 74.6363 Evaluate side-chains 234 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 660 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 223 ASN A 254 HIS A 319 ASN A 408 ASN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN B 223 ASN B 327 GLN ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN B 674 HIS C 222 ASN ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 HIS C 568 GLN C 583 ASN C 628 GLN C 633 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113027 restraints weight = 19166.550| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.21 r_work: 0.3159 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16043 Z= 0.126 Angle : 0.526 5.708 21818 Z= 0.290 Chirality : 0.044 0.214 2421 Planarity : 0.005 0.065 2791 Dihedral : 5.267 55.533 2202 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.75 % Allowed : 7.17 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.18), residues: 1936 helix: -0.73 (0.27), residues: 311 sheet: -1.99 (0.20), residues: 550 loop : -0.98 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 573 TYR 0.026 0.002 TYR B 385 PHE 0.019 0.002 PHE L 61 TRP 0.014 0.001 TRP H 112 HIS 0.015 0.001 HIS B 674 Details of bonding type rmsd covalent geometry : bond 0.00281 (16026) covalent geometry : angle 0.52574 (21784) SS BOND : bond 0.00261 ( 17) SS BOND : angle 0.86821 ( 34) hydrogen bonds : bond 0.04168 ( 546) hydrogen bonds : angle 5.62827 ( 1599) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.7948 (m-80) cc_final: 0.7732 (m-80) REVERT: A 150 GLU cc_start: 0.7803 (pm20) cc_final: 0.7184 (tt0) REVERT: A 281 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8557 (mt-10) REVERT: A 339 ARG cc_start: 0.8376 (mtt-85) cc_final: 0.7838 (mtt90) REVERT: A 365 ARG cc_start: 0.7932 (ttp-110) cc_final: 0.7403 (mmt180) REVERT: A 416 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7245 (pp30) REVERT: A 634 GLU cc_start: 0.7930 (tt0) cc_final: 0.7639 (mt-10) REVERT: A 649 HIS cc_start: 0.8200 (t-90) cc_final: 0.7867 (t-170) REVERT: A 665 TYR cc_start: 0.7157 (m-80) cc_final: 0.6499 (m-80) REVERT: A 688 THR cc_start: 0.8888 (m) cc_final: 0.8515 (p) REVERT: A 691 LYS cc_start: 0.9105 (mmpt) cc_final: 0.8850 (mmtm) REVERT: B 138 THR cc_start: 0.8819 (t) cc_final: 0.8558 (p) REVERT: B 166 LYS cc_start: 0.8874 (ptmm) cc_final: 0.8534 (ptpp) REVERT: B 229 PHE cc_start: 0.8563 (m-10) cc_final: 0.8360 (m-10) REVERT: B 256 THR cc_start: 0.8930 (m) cc_final: 0.8489 (p) REVERT: B 408 ASN cc_start: 0.7941 (t0) cc_final: 0.7697 (t0) REVERT: B 661 TYR cc_start: 0.7260 (t80) cc_final: 0.7047 (t80) REVERT: C 241 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.7784 (pt) REVERT: C 314 TYR cc_start: 0.8126 (p90) cc_final: 0.7835 (p90) REVERT: C 343 GLU cc_start: 0.8499 (mp0) cc_final: 0.8276 (mt-10) REVERT: C 403 GLU cc_start: 0.7260 (pm20) cc_final: 0.6712 (pt0) REVERT: C 419 LYS cc_start: 0.7651 (mppt) cc_final: 0.7382 (mmmm) REVERT: C 420 GLU cc_start: 0.8164 (tp30) cc_final: 0.7932 (tm-30) REVERT: C 433 ARG cc_start: 0.8124 (ttt180) cc_final: 0.7874 (mtp85) REVERT: C 573 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.7191 (mtm110) REVERT: C 650 LYS cc_start: 0.7526 (mtpp) cc_final: 0.6992 (ttmm) REVERT: C 674 HIS cc_start: 0.7428 (p-80) cc_final: 0.6834 (t-170) REVERT: C 716 GLU cc_start: 0.8543 (tp30) cc_final: 0.8025 (tp30) outliers start: 30 outliers final: 15 residues processed: 264 average time/residue: 0.1217 time to fit residues: 47.9614 Evaluate side-chains 210 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 122 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 chunk 100 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 159 optimal weight: 20.0000 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 HIS B 254 HIS ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** 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 = 0.3781 r_free = 0.3781 target = 0.152903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112920 restraints weight = 19432.688| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.22 r_work: 0.3160 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16043 Z= 0.111 Angle : 0.481 5.806 21818 Z= 0.263 Chirality : 0.042 0.196 2421 Planarity : 0.004 0.060 2791 Dihedral : 4.756 51.790 2200 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.63 % Allowed : 9.15 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.19), residues: 1936 helix: 0.56 (0.30), residues: 316 sheet: -1.49 (0.21), residues: 555 loop : -0.65 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 365 TYR 0.027 0.001 TYR C 385 PHE 0.017 0.002 PHE C 148 TRP 0.011 0.001 TRP H 112 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00254 (16026) covalent geometry : angle 0.48069 (21784) SS BOND : bond 0.00312 ( 17) SS BOND : angle 0.77808 ( 34) hydrogen bonds : bond 0.03447 ( 546) hydrogen bonds : angle 5.00683 ( 1599) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.7760 (pm20) cc_final: 0.7315 (tt0) REVERT: A 339 ARG cc_start: 0.8391 (mtt-85) cc_final: 0.7841 (mtt90) REVERT: A 365 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7481 (mmt180) REVERT: A 573 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7732 (ttm-80) REVERT: A 634 GLU cc_start: 0.7945 (tt0) cc_final: 0.7666 (mt-10) REVERT: A 649 HIS cc_start: 0.8117 (t-90) cc_final: 0.7742 (t70) REVERT: A 665 TYR cc_start: 0.7110 (m-80) cc_final: 0.6704 (m-80) REVERT: A 688 THR cc_start: 0.8890 (m) cc_final: 0.8613 (p) REVERT: A 691 LYS cc_start: 0.9156 (mmpt) cc_final: 0.8892 (mmtm) REVERT: A 723 MET cc_start: 0.7452 (ttp) cc_final: 0.6914 (ttm) REVERT: B 119 PHE cc_start: 0.8359 (m-80) cc_final: 0.8074 (m-80) REVERT: B 130 ILE cc_start: 0.7581 (pt) cc_final: 0.7271 (mt) REVERT: B 166 LYS cc_start: 0.8861 (ptmm) cc_final: 0.8479 (ptpp) REVERT: B 229 PHE cc_start: 0.8557 (m-10) cc_final: 0.8351 (m-10) REVERT: B 256 THR cc_start: 0.8975 (m) cc_final: 0.8500 (p) REVERT: B 365 ARG cc_start: 0.8706 (ptt90) cc_final: 0.7930 (ptp-110) REVERT: B 403 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: B 582 SER cc_start: 0.7721 (t) cc_final: 0.7518 (m) REVERT: B 721 ASN cc_start: 0.8204 (m-40) cc_final: 0.7784 (m-40) REVERT: C 183 SER cc_start: 0.8560 (m) cc_final: 0.8177 (p) REVERT: C 314 TYR cc_start: 0.8110 (p90) cc_final: 0.7765 (p90) REVERT: C 343 GLU cc_start: 0.8480 (mp0) cc_final: 0.8266 (mt-10) REVERT: C 393 MET cc_start: 0.8614 (mtt) cc_final: 0.8278 (mtt) REVERT: C 403 GLU cc_start: 0.7145 (pm20) cc_final: 0.6494 (pt0) REVERT: C 419 LYS cc_start: 0.7826 (mppt) cc_final: 0.7592 (mmmm) REVERT: C 573 ARG cc_start: 0.7578 (mtp-110) cc_final: 0.7260 (mtm110) REVERT: C 674 HIS cc_start: 0.7418 (p-80) cc_final: 0.6863 (t-170) REVERT: C 708 ASP cc_start: 0.8428 (t70) cc_final: 0.7932 (t0) REVERT: C 716 GLU cc_start: 0.8505 (tp30) cc_final: 0.7996 (tp30) REVERT: H 74 ASN cc_start: 0.7198 (m-40) cc_final: 0.6975 (m-40) outliers start: 28 outliers final: 19 residues processed: 230 average time/residue: 0.1197 time to fit residues: 40.4081 Evaluate side-chains 204 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 44 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108652 restraints weight = 19531.457| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.31 r_work: 0.3093 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16043 Z= 0.233 Angle : 0.549 5.616 21818 Z= 0.298 Chirality : 0.045 0.219 2421 Planarity : 0.004 0.059 2791 Dihedral : 4.995 53.627 2200 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.33 % Allowed : 9.67 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.19), residues: 1936 helix: 0.80 (0.31), residues: 313 sheet: -1.30 (0.21), residues: 565 loop : -0.55 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 382 TYR 0.020 0.002 TYR C 385 PHE 0.025 0.002 PHE B 695 TRP 0.018 0.001 TRP H 112 HIS 0.007 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00569 (16026) covalent geometry : angle 0.54831 (21784) SS BOND : bond 0.00266 ( 17) SS BOND : angle 0.76511 ( 34) hydrogen bonds : bond 0.03719 ( 546) hydrogen bonds : angle 5.23449 ( 1599) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.7772 (pm20) cc_final: 0.7340 (tt0) REVERT: A 339 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.7801 (mtt90) REVERT: A 365 ARG cc_start: 0.7853 (ttp-110) cc_final: 0.7403 (mmt180) REVERT: A 573 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7660 (ttm-80) REVERT: A 634 GLU cc_start: 0.7986 (tt0) cc_final: 0.7616 (mt-10) REVERT: A 665 TYR cc_start: 0.7252 (m-80) cc_final: 0.6552 (m-80) REVERT: A 688 THR cc_start: 0.8949 (m) cc_final: 0.8587 (p) REVERT: A 691 LYS cc_start: 0.9118 (mmpt) cc_final: 0.8892 (mmtm) REVERT: B 166 LYS cc_start: 0.8869 (ptmm) cc_final: 0.8633 (ptpp) REVERT: B 327 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: B 461 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7669 (tt) REVERT: B 582 SER cc_start: 0.7669 (t) cc_final: 0.7427 (m) REVERT: B 661 TYR cc_start: 0.7234 (t80) cc_final: 0.7018 (t80) REVERT: B 721 ASN cc_start: 0.8193 (m-40) cc_final: 0.7821 (m-40) REVERT: C 183 SER cc_start: 0.8567 (m) cc_final: 0.8225 (p) REVERT: C 314 TYR cc_start: 0.8123 (p90) cc_final: 0.7485 (p90) REVERT: C 343 GLU cc_start: 0.8426 (mp0) cc_final: 0.8221 (mt-10) REVERT: C 378 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7336 (mp0) REVERT: C 389 PHE cc_start: 0.8340 (m-80) cc_final: 0.8098 (m-80) REVERT: C 419 LYS cc_start: 0.8032 (mppt) cc_final: 0.7660 (mmmt) REVERT: C 435 ASN cc_start: 0.6879 (t0) cc_final: 0.5730 (p0) REVERT: C 674 HIS cc_start: 0.7437 (p-80) cc_final: 0.6885 (t-170) REVERT: C 708 ASP cc_start: 0.8394 (t70) cc_final: 0.7980 (t0) REVERT: C 716 GLU cc_start: 0.8536 (tp30) cc_final: 0.7956 (tp30) REVERT: H 74 ASN cc_start: 0.7300 (m-40) cc_final: 0.7015 (m-40) REVERT: H 102 TYR cc_start: 0.8139 (p90) cc_final: 0.7796 (p90) REVERT: H 114 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7241 (pt0) outliers start: 40 outliers final: 26 residues processed: 215 average time/residue: 0.1086 time to fit residues: 35.7480 Evaluate side-chains 199 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 417 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 437 SER Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 133 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 35 optimal weight: 0.0010 chunk 12 optimal weight: 0.2980 chunk 142 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 149 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 191 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.152758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112814 restraints weight = 19367.836| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.21 r_work: 0.3157 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16043 Z= 0.084 Angle : 0.443 5.836 21818 Z= 0.241 Chirality : 0.041 0.170 2421 Planarity : 0.004 0.059 2791 Dihedral : 4.500 51.698 2200 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.52 % Allowed : 10.37 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 1936 helix: 1.29 (0.32), residues: 314 sheet: -1.05 (0.22), residues: 566 loop : -0.30 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 365 TYR 0.017 0.001 TYR H 27 PHE 0.012 0.001 PHE C 293 TRP 0.010 0.001 TRP L 90 HIS 0.012 0.001 HIS B 649 Details of bonding type rmsd covalent geometry : bond 0.00183 (16026) covalent geometry : angle 0.44275 (21784) SS BOND : bond 0.00193 ( 17) SS BOND : angle 0.55901 ( 34) hydrogen bonds : bond 0.02902 ( 546) hydrogen bonds : angle 4.65006 ( 1599) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.460 Fit side-chains REVERT: A 150 GLU cc_start: 0.7772 (pm20) cc_final: 0.7340 (tt0) REVERT: A 339 ARG cc_start: 0.8401 (mtt-85) cc_final: 0.7849 (mtt90) REVERT: A 365 ARG cc_start: 0.7924 (ttp-110) cc_final: 0.7351 (mmt180) REVERT: A 573 ARG cc_start: 0.7904 (ttm110) cc_final: 0.7634 (ttm-80) REVERT: A 634 GLU cc_start: 0.7949 (tt0) cc_final: 0.7598 (mt-10) REVERT: A 665 TYR cc_start: 0.6968 (m-80) cc_final: 0.6682 (m-80) REVERT: A 688 THR cc_start: 0.8900 (m) cc_final: 0.8622 (p) REVERT: A 691 LYS cc_start: 0.9146 (mmpt) cc_final: 0.8771 (mmtm) REVERT: A 708 ASP cc_start: 0.8237 (t70) cc_final: 0.7708 (t0) REVERT: B 166 LYS cc_start: 0.8859 (ptmm) cc_final: 0.8460 (ptpp) REVERT: B 229 PHE cc_start: 0.8506 (m-10) cc_final: 0.8274 (m-10) REVERT: B 365 ARG cc_start: 0.8783 (ptt90) cc_final: 0.8059 (ptp-110) REVERT: B 461 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7669 (tt) REVERT: B 554 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7445 (t80) REVERT: B 582 SER cc_start: 0.7667 (t) cc_final: 0.7442 (m) REVERT: B 661 TYR cc_start: 0.7176 (t80) cc_final: 0.6786 (t80) REVERT: C 314 TYR cc_start: 0.8066 (p90) cc_final: 0.7565 (p90) REVERT: C 393 MET cc_start: 0.8535 (mtt) cc_final: 0.8237 (mtt) REVERT: C 419 LYS cc_start: 0.7992 (mppt) cc_final: 0.7600 (mmtt) REVERT: C 435 ASN cc_start: 0.6789 (t0) cc_final: 0.5753 (p0) REVERT: C 554 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: C 573 ARG cc_start: 0.7544 (mtp-110) cc_final: 0.7249 (mtm110) REVERT: C 665 TYR cc_start: 0.7907 (m-80) cc_final: 0.7596 (m-80) REVERT: C 674 HIS cc_start: 0.7419 (p-80) cc_final: 0.6830 (t-170) REVERT: C 708 ASP cc_start: 0.8355 (t70) cc_final: 0.7902 (t0) REVERT: C 716 GLU cc_start: 0.8511 (tp30) cc_final: 0.7859 (tp30) REVERT: H 10 GLU cc_start: 0.7885 (mp0) cc_final: 0.7326 (mp0) REVERT: H 102 TYR cc_start: 0.8081 (p90) cc_final: 0.7774 (p90) REVERT: L 36 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7248 (tt0) outliers start: 26 outliers final: 14 residues processed: 212 average time/residue: 0.1170 time to fit residues: 37.6290 Evaluate side-chains 190 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain B residue 261 MET Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 55 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 2 optimal weight: 0.0870 chunk 21 optimal weight: 0.4980 chunk 165 optimal weight: 0.0970 chunk 40 optimal weight: 0.2980 chunk 129 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 184 optimal weight: 0.0040 overall best weight: 0.1968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 ASN ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.155099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.115972 restraints weight = 19261.056| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.42 r_work: 0.3188 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16043 Z= 0.077 Angle : 0.432 5.802 21818 Z= 0.234 Chirality : 0.041 0.164 2421 Planarity : 0.004 0.057 2791 Dihedral : 4.027 47.034 2198 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.22 % Allowed : 11.01 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1936 helix: 1.56 (0.32), residues: 314 sheet: -0.91 (0.22), residues: 572 loop : -0.15 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 365 TYR 0.023 0.001 TYR H 95 PHE 0.010 0.001 PHE B 165 TRP 0.010 0.001 TRP L 90 HIS 0.009 0.001 HIS B 649 Details of bonding type rmsd covalent geometry : bond 0.00165 (16026) covalent geometry : angle 0.42978 (21784) SS BOND : bond 0.00177 ( 17) SS BOND : angle 1.08447 ( 34) hydrogen bonds : bond 0.02692 ( 546) hydrogen bonds : angle 4.42406 ( 1599) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.585 Fit side-chains REVERT: A 150 GLU cc_start: 0.7782 (pm20) cc_final: 0.7499 (tt0) REVERT: A 339 ARG cc_start: 0.8405 (mtt-85) cc_final: 0.7905 (mtt90) REVERT: A 365 ARG cc_start: 0.7929 (ttp-110) cc_final: 0.7597 (mmt180) REVERT: A 573 ARG cc_start: 0.7997 (ttm110) cc_final: 0.7746 (ttm-80) REVERT: A 665 TYR cc_start: 0.7184 (m-80) cc_final: 0.6727 (m-80) REVERT: A 691 LYS cc_start: 0.9250 (mmpt) cc_final: 0.8920 (mmtm) REVERT: A 708 ASP cc_start: 0.8351 (t70) cc_final: 0.7855 (t0) REVERT: B 140 PRO cc_start: 0.8115 (Cg_endo) cc_final: 0.7799 (Cg_exo) REVERT: B 166 LYS cc_start: 0.8810 (ptmm) cc_final: 0.8475 (ptpp) REVERT: B 365 ARG cc_start: 0.8775 (ptt90) cc_final: 0.8132 (ptp-110) REVERT: B 461 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7753 (tt) REVERT: B 531 MET cc_start: 0.8504 (mmp) cc_final: 0.8185 (mmp) REVERT: B 554 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7647 (t80) REVERT: B 571 LYS cc_start: 0.8044 (ttpp) cc_final: 0.7820 (tmmt) REVERT: B 661 TYR cc_start: 0.7429 (t80) cc_final: 0.6981 (t80) REVERT: C 314 TYR cc_start: 0.8140 (p90) cc_final: 0.7678 (p90) REVERT: C 393 MET cc_start: 0.8552 (mtt) cc_final: 0.8318 (mtt) REVERT: C 419 LYS cc_start: 0.8082 (mppt) cc_final: 0.7740 (mmtt) REVERT: C 435 ASN cc_start: 0.6808 (t0) cc_final: 0.5906 (p0) REVERT: C 554 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: C 573 ARG cc_start: 0.7734 (mtp-110) cc_final: 0.7460 (mtm110) REVERT: C 674 HIS cc_start: 0.7435 (p-80) cc_final: 0.6870 (t-170) REVERT: C 716 GLU cc_start: 0.8480 (tp30) cc_final: 0.8029 (tp30) REVERT: H 10 GLU cc_start: 0.7906 (mp0) cc_final: 0.7455 (mp0) REVERT: H 80 TYR cc_start: 0.7273 (m-10) cc_final: 0.7071 (m-10) REVERT: H 102 TYR cc_start: 0.8217 (p90) cc_final: 0.7932 (p90) outliers start: 21 outliers final: 15 residues processed: 211 average time/residue: 0.1138 time to fit residues: 35.8902 Evaluate side-chains 191 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 103 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 154 optimal weight: 0.0060 chunk 181 optimal weight: 0.2980 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.0570 chunk 177 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 ASN C 525 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115199 restraints weight = 19275.668| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.35 r_work: 0.3196 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16043 Z= 0.078 Angle : 0.432 6.676 21818 Z= 0.233 Chirality : 0.041 0.145 2421 Planarity : 0.003 0.056 2791 Dihedral : 3.923 46.020 2198 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.28 % Allowed : 11.54 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1936 helix: 1.72 (0.31), residues: 314 sheet: -0.80 (0.22), residues: 572 loop : -0.04 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 365 TYR 0.021 0.001 TYR H 95 PHE 0.010 0.001 PHE B 165 TRP 0.010 0.001 TRP L 90 HIS 0.009 0.001 HIS B 649 Details of bonding type rmsd covalent geometry : bond 0.00172 (16026) covalent geometry : angle 0.42966 (21784) SS BOND : bond 0.00282 ( 17) SS BOND : angle 1.16949 ( 34) hydrogen bonds : bond 0.02661 ( 546) hydrogen bonds : angle 4.35554 ( 1599) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.580 Fit side-chains REVERT: A 150 GLU cc_start: 0.7773 (pm20) cc_final: 0.7480 (tt0) REVERT: A 339 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.7893 (mtt90) REVERT: A 365 ARG cc_start: 0.7961 (ttp-110) cc_final: 0.7469 (mmt180) REVERT: A 416 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7439 (pp30) REVERT: A 573 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7689 (ttm-80) REVERT: A 649 HIS cc_start: 0.7987 (t70) cc_final: 0.7777 (t-170) REVERT: A 665 TYR cc_start: 0.7185 (m-80) cc_final: 0.6590 (m-80) REVERT: A 691 LYS cc_start: 0.9217 (mmpt) cc_final: 0.8881 (mmtm) REVERT: A 723 MET cc_start: 0.7378 (ttp) cc_final: 0.7103 (ttm) REVERT: B 140 PRO cc_start: 0.8039 (Cg_endo) cc_final: 0.7718 (Cg_exo) REVERT: B 166 LYS cc_start: 0.8823 (ptmm) cc_final: 0.8458 (ptpp) REVERT: B 365 ARG cc_start: 0.8813 (ptt90) cc_final: 0.8136 (ptp-110) REVERT: B 405 ASN cc_start: 0.8153 (m-40) cc_final: 0.7377 (p0) REVERT: B 461 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7674 (tt) REVERT: B 531 MET cc_start: 0.8550 (mmp) cc_final: 0.8120 (mmp) REVERT: B 554 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7650 (t80) REVERT: B 577 ASP cc_start: 0.8741 (t0) cc_final: 0.8373 (t0) REVERT: B 661 TYR cc_start: 0.7346 (t80) cc_final: 0.6895 (t80) REVERT: C 314 TYR cc_start: 0.8115 (p90) cc_final: 0.7674 (p90) REVERT: C 378 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7258 (mp0) REVERT: C 393 MET cc_start: 0.8483 (mtt) cc_final: 0.8251 (mtt) REVERT: C 419 LYS cc_start: 0.8024 (mppt) cc_final: 0.7722 (mmtt) REVERT: C 435 ASN cc_start: 0.6771 (t0) cc_final: 0.5917 (p0) REVERT: C 554 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: C 573 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7398 (mtm110) REVERT: C 674 HIS cc_start: 0.7420 (p-80) cc_final: 0.6827 (t-170) REVERT: C 716 GLU cc_start: 0.8498 (tp30) cc_final: 0.7952 (tp30) REVERT: H 10 GLU cc_start: 0.7906 (mp0) cc_final: 0.7399 (mp0) REVERT: H 39 GLN cc_start: 0.7435 (tt0) cc_final: 0.7138 (tt0) REVERT: H 102 TYR cc_start: 0.8171 (p90) cc_final: 0.7883 (p90) REVERT: L 36 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7021 (tt0) outliers start: 22 outliers final: 14 residues processed: 207 average time/residue: 0.1159 time to fit residues: 36.1837 Evaluate side-chains 197 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 180 TRP Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 102 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN C 427 ASN C 525 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109600 restraints weight = 19470.049| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.09 r_work: 0.3112 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16043 Z= 0.195 Angle : 0.524 7.166 21818 Z= 0.282 Chirality : 0.044 0.165 2421 Planarity : 0.004 0.054 2791 Dihedral : 4.395 45.482 2198 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.52 % Allowed : 11.54 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.19), residues: 1936 helix: 1.45 (0.31), residues: 311 sheet: -0.86 (0.22), residues: 565 loop : -0.10 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 573 TYR 0.021 0.002 TYR H 27 PHE 0.021 0.002 PHE B 293 TRP 0.014 0.001 TRP H 112 HIS 0.011 0.001 HIS B 649 Details of bonding type rmsd covalent geometry : bond 0.00474 (16026) covalent geometry : angle 0.52088 (21784) SS BOND : bond 0.00480 ( 17) SS BOND : angle 1.51309 ( 34) hydrogen bonds : bond 0.03387 ( 546) hydrogen bonds : angle 4.90569 ( 1599) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.649 Fit side-chains REVERT: A 150 GLU cc_start: 0.7816 (pm20) cc_final: 0.7405 (tt0) REVERT: A 339 ARG cc_start: 0.8386 (mtt-85) cc_final: 0.7861 (mtt90) REVERT: A 365 ARG cc_start: 0.7835 (ttp-110) cc_final: 0.7296 (mmt180) REVERT: A 416 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7461 (pp30) REVERT: A 649 HIS cc_start: 0.7938 (t70) cc_final: 0.7731 (t-170) REVERT: A 665 TYR cc_start: 0.7160 (m-80) cc_final: 0.6639 (m-80) REVERT: A 691 LYS cc_start: 0.9121 (mmpt) cc_final: 0.8786 (mmtm) REVERT: B 166 LYS cc_start: 0.8838 (ptmm) cc_final: 0.8607 (ptpp) REVERT: B 229 PHE cc_start: 0.8647 (m-10) cc_final: 0.8423 (m-10) REVERT: B 461 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7638 (tt) REVERT: B 554 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7473 (t80) REVERT: B 661 TYR cc_start: 0.7295 (t80) cc_final: 0.6941 (t80) REVERT: C 314 TYR cc_start: 0.8083 (p90) cc_final: 0.7870 (p90) REVERT: C 378 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7354 (mp0) REVERT: C 419 LYS cc_start: 0.8052 (mppt) cc_final: 0.7690 (mmtt) REVERT: C 435 ASN cc_start: 0.6899 (t0) cc_final: 0.5912 (p0) REVERT: C 554 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: C 573 ARG cc_start: 0.7559 (mtp-110) cc_final: 0.7279 (mtm110) REVERT: C 674 HIS cc_start: 0.7434 (p-80) cc_final: 0.6809 (t-170) REVERT: C 716 GLU cc_start: 0.8485 (tp30) cc_final: 0.7848 (tp30) REVERT: H 10 GLU cc_start: 0.7903 (mp0) cc_final: 0.7178 (mp0) REVERT: H 102 TYR cc_start: 0.8228 (p90) cc_final: 0.7964 (p90) outliers start: 26 outliers final: 18 residues processed: 197 average time/residue: 0.1129 time to fit residues: 33.2294 Evaluate side-chains 189 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 GLN Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 55 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN C 427 ASN H 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111336 restraints weight = 19452.539| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.30 r_work: 0.3127 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16043 Z= 0.108 Angle : 0.461 7.693 21818 Z= 0.249 Chirality : 0.042 0.142 2421 Planarity : 0.004 0.056 2791 Dihedral : 4.175 45.365 2198 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.34 % Allowed : 11.89 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1936 helix: 1.58 (0.31), residues: 314 sheet: -0.76 (0.22), residues: 566 loop : -0.04 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 573 TYR 0.020 0.001 TYR H 95 PHE 0.014 0.001 PHE B 293 TRP 0.010 0.001 TRP B 359 HIS 0.010 0.001 HIS B 649 Details of bonding type rmsd covalent geometry : bond 0.00253 (16026) covalent geometry : angle 0.45969 (21784) SS BOND : bond 0.00289 ( 17) SS BOND : angle 1.10521 ( 34) hydrogen bonds : bond 0.02957 ( 546) hydrogen bonds : angle 4.60597 ( 1599) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.609 Fit side-chains REVERT: A 150 GLU cc_start: 0.7829 (pm20) cc_final: 0.7496 (tt0) REVERT: A 339 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.7935 (mtt90) REVERT: A 365 ARG cc_start: 0.7897 (ttp-110) cc_final: 0.7454 (mmt180) REVERT: A 416 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7503 (pp30) REVERT: A 665 TYR cc_start: 0.7116 (m-80) cc_final: 0.6631 (m-80) REVERT: A 691 LYS cc_start: 0.9209 (mmpt) cc_final: 0.8873 (mmtm) REVERT: B 166 LYS cc_start: 0.8871 (ptmm) cc_final: 0.8654 (ptpp) REVERT: B 229 PHE cc_start: 0.8572 (m-10) cc_final: 0.8316 (m-10) REVERT: B 365 ARG cc_start: 0.8824 (ptt90) cc_final: 0.8174 (ptp-110) REVERT: B 461 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7770 (tt) REVERT: B 554 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7691 (t80) REVERT: B 571 LYS cc_start: 0.7864 (tmmt) cc_final: 0.7609 (ttpp) REVERT: B 661 TYR cc_start: 0.7456 (t80) cc_final: 0.7074 (t80) REVERT: C 393 MET cc_start: 0.8726 (mtt) cc_final: 0.8479 (mtt) REVERT: C 419 LYS cc_start: 0.8093 (mppt) cc_final: 0.7852 (mmmt) REVERT: C 435 ASN cc_start: 0.6908 (t0) cc_final: 0.5959 (p0) REVERT: C 554 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: C 573 ARG cc_start: 0.7700 (mtp-110) cc_final: 0.7428 (mtm110) REVERT: C 674 HIS cc_start: 0.7462 (p-80) cc_final: 0.6823 (t-170) REVERT: C 716 GLU cc_start: 0.8497 (tp30) cc_final: 0.7993 (tp30) REVERT: H 10 GLU cc_start: 0.7955 (mp0) cc_final: 0.7367 (mp0) REVERT: H 102 TYR cc_start: 0.8337 (p90) cc_final: 0.8098 (p90) outliers start: 23 outliers final: 17 residues processed: 196 average time/residue: 0.1146 time to fit residues: 33.8167 Evaluate side-chains 193 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 119 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 ASN C 628 GLN ** C 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111872 restraints weight = 19296.407| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.19 r_work: 0.3142 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16043 Z= 0.110 Angle : 0.461 8.238 21818 Z= 0.249 Chirality : 0.042 0.138 2421 Planarity : 0.004 0.055 2791 Dihedral : 4.109 44.699 2198 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.34 % Allowed : 11.95 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1936 helix: 1.72 (0.31), residues: 314 sheet: -0.74 (0.22), residues: 565 loop : -0.03 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 573 TYR 0.019 0.001 TYR H 95 PHE 0.014 0.001 PHE B 293 TRP 0.009 0.001 TRP B 359 HIS 0.010 0.001 HIS B 649 Details of bonding type rmsd covalent geometry : bond 0.00261 (16026) covalent geometry : angle 0.45948 (21784) SS BOND : bond 0.00228 ( 17) SS BOND : angle 1.05903 ( 34) hydrogen bonds : bond 0.02885 ( 546) hydrogen bonds : angle 4.55249 ( 1599) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.613 Fit side-chains REVERT: A 150 GLU cc_start: 0.7810 (pm20) cc_final: 0.7538 (tt0) REVERT: A 339 ARG cc_start: 0.8402 (mtt-85) cc_final: 0.7927 (mtt90) REVERT: A 365 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7429 (mmt180) REVERT: A 416 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7456 (pp30) REVERT: A 691 LYS cc_start: 0.9211 (mmpt) cc_final: 0.8884 (mmtm) REVERT: B 166 LYS cc_start: 0.8867 (ptmm) cc_final: 0.8578 (ptpp) REVERT: B 229 PHE cc_start: 0.8569 (m-10) cc_final: 0.8319 (m-10) REVERT: B 365 ARG cc_start: 0.8819 (ptt90) cc_final: 0.8179 (ptp-110) REVERT: B 461 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7797 (tt) REVERT: B 554 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7736 (t80) REVERT: B 571 LYS cc_start: 0.7862 (tmmt) cc_final: 0.7610 (ttpp) REVERT: B 661 TYR cc_start: 0.7472 (t80) cc_final: 0.7094 (t80) REVERT: C 378 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7369 (mp0) REVERT: C 393 MET cc_start: 0.8716 (mtt) cc_final: 0.8461 (mtt) REVERT: C 435 ASN cc_start: 0.6903 (t0) cc_final: 0.6019 (p0) REVERT: C 554 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: C 573 ARG cc_start: 0.7697 (mtp-110) cc_final: 0.7428 (mtm110) REVERT: C 674 HIS cc_start: 0.7450 (p-80) cc_final: 0.6806 (t-170) REVERT: C 716 GLU cc_start: 0.8515 (tp30) cc_final: 0.8020 (tp30) REVERT: H 10 GLU cc_start: 0.7955 (mp0) cc_final: 0.7350 (mp0) REVERT: H 102 TYR cc_start: 0.8343 (p90) cc_final: 0.8107 (p90) outliers start: 23 outliers final: 18 residues processed: 193 average time/residue: 0.1164 time to fit residues: 34.1395 Evaluate side-chains 190 residues out of total 1754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 645 CYS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 132 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 104 optimal weight: 0.0670 chunk 28 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN C 427 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109592 restraints weight = 19433.938| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.17 r_work: 0.3120 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16043 Z= 0.159 Angle : 0.498 8.185 21818 Z= 0.267 Chirality : 0.043 0.141 2421 Planarity : 0.004 0.055 2791 Dihedral : 4.284 44.921 2198 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.57 % Allowed : 11.66 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 1936 helix: 1.59 (0.31), residues: 314 sheet: -0.74 (0.22), residues: 567 loop : -0.05 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 573 TYR 0.038 0.001 TYR A 665 PHE 0.019 0.002 PHE B 293 TRP 0.010 0.001 TRP H 112 HIS 0.010 0.001 HIS B 649 Details of bonding type rmsd covalent geometry : bond 0.00385 (16026) covalent geometry : angle 0.49572 (21784) SS BOND : bond 0.00267 ( 17) SS BOND : angle 1.20069 ( 34) hydrogen bonds : bond 0.03133 ( 546) hydrogen bonds : angle 4.71671 ( 1599) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4404.42 seconds wall clock time: 75 minutes 54.23 seconds (4554.23 seconds total)