Starting phenix.real_space_refine on Mon Aug 25 03:46:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vj6_43275/08_2025/8vj6_43275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vj6_43275/08_2025/8vj6_43275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vj6_43275/08_2025/8vj6_43275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vj6_43275/08_2025/8vj6_43275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vj6_43275/08_2025/8vj6_43275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vj6_43275/08_2025/8vj6_43275.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 120 5.16 5 C 16153 2.51 5 N 4167 2.21 5 O 4736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.13s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25176 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6279 Classifications: {'peptide': 797} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 773} Chain breaks: 2 Chain: "B" Number of atoms: 6267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6267 Classifications: {'peptide': 796} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 772} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 6279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6279 Classifications: {'peptide': 797} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 773} Chain breaks: 2 Chain: "D" Number of atoms: 6263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6263 Classifications: {'peptide': 796} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 772} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'A1AB5': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'A1AB5': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.69, per 1000 atoms: 0.23 Number of scatterers: 25176 At special positions: 0 Unit cell: (123.69, 160.89, 187.86, 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 120 16.00 O 4736 8.00 N 4167 7.00 C 16153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 991.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5852 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 31 sheets defined 48.4% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.915A pdb=" N LEU A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.558A pdb=" N GLY A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.793A pdb=" N PHE A 237 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.885A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.515A pdb=" N ILE A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 removed outlier: 4.000A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.703A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 521 Proline residue: A 520 - end of helix Processing helix chain 'A' and resid 522 through 545 Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.920A pdb=" N THR A 568 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 569' Processing helix chain 'A' and resid 572 through 586 Processing helix chain 'A' and resid 595 through 628 Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 767 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 820 removed outlier: 3.635A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 819 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.572A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.665A pdb=" N GLY B 230 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASP B 231 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 removed outlier: 4.605A pdb=" N PHE B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.776A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.941A pdb=" N GLY B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 521 Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 625 Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.597A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.723A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 769 through 771 No H-bonds generated for 'chain 'B' and resid 769 through 771' Processing helix chain 'B' and resid 773 through 778 removed outlier: 4.225A pdb=" N ASP B 777 " --> pdb=" O CYS B 773 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 778 " --> pdb=" O GLY B 774 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 773 through 778' Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 818 removed outlier: 3.814A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 117 through 128 removed outlier: 3.781A pdb=" N LEU C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 176 through 187 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.608A pdb=" N PHE C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.766A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.694A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 4.001A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 521 Proline residue: C 520 - end of helix Processing helix chain 'C' and resid 522 through 545 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 Processing helix chain 'C' and resid 637 through 641 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.618A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.995A pdb=" N ALA C 691 " --> pdb=" O ALA C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 767 Processing helix chain 'C' and resid 782 through 786 removed outlier: 3.516A pdb=" N ALA C 786 " --> pdb=" O LYS C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.723A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 54 through 68 removed outlier: 3.744A pdb=" N ARG D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 143 through 157 Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 232 through 237 removed outlier: 4.305A pdb=" N PHE D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 263 removed outlier: 3.748A pdb=" N ARG D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.468A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.798A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 4.025A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA D 433 " --> pdb=" O ALA D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 467 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.769A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 521 Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 572 through 586 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.690A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.884A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.822A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 818 removed outlier: 3.689A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 50 removed outlier: 6.524A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N HIS A 46 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 14 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ASP A 48 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY A 16 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU A 50 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N PHE A 18 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N ALA A 72 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 7.468A pdb=" N PHE A 133 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE A 163 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR A 135 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 340 removed outlier: 4.090A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 399 removed outlier: 6.643A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA7, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.828A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.320A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 50 removed outlier: 6.753A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU B 50 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE B 18 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLN B 13 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N PHE B 74 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 164 removed outlier: 7.422A pdb=" N LYS B 132 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N ILE B 193 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 134 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASP B 195 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 136 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AB3, first strand: chain 'B' and resid 395 through 399 removed outlier: 5.906A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 407 through 408 removed outlier: 3.744A pdb=" N GLU B 422 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.002A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 475 through 480 removed outlier: 9.002A pdb=" N ALA B 475 " --> pdb=" O PRO B 737 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.492A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 43 through 50 removed outlier: 6.213A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.188A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE C 358 " --> pdb=" O TYR C 373 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR C 373 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE C 360 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 338 through 340 removed outlier: 3.853A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 395 through 399 Processing sheet with id=AC3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC4, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC5, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.927A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.435A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 42 through 50 removed outlier: 6.509A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 159 through 164 removed outlier: 7.498A pdb=" N LYS D 132 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ILE D 193 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA D 134 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASP D 195 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU D 136 " --> pdb=" O ASP D 195 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 358 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR D 373 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE D 360 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 338 through 340 removed outlier: 3.852A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 440 through 444 removed outlier: 4.212A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AD3, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.418A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR D 732 " --> pdb=" O MET D 496 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.441A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1199 hydrogen bonds defined for protein. 3447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.99 Time building geometry restraints manager: 2.24 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: 5905 1.33 - 1.45: 5651 1.45 - 1.57: 13959 1.57 - 1.70: 0 1.70 - 1.82: 196 Bond restraints: 25711 Sorted by residual: bond pdb=" C2 A1AB5 A1402 " pdb=" N1 A1AB5 A1402 " ideal model delta sigma weight residual 1.275 1.455 -0.180 2.00e-02 2.50e+03 8.13e+01 bond pdb=" C2 A1AB5 A1401 " pdb=" N1 A1AB5 A1401 " ideal model delta sigma weight residual 1.275 1.453 -0.178 2.00e-02 2.50e+03 7.94e+01 bond pdb=" C2 A1AB5 C1401 " pdb=" N1 A1AB5 C1401 " ideal model delta sigma weight residual 1.275 1.453 -0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C2 A1AB5 C1402 " pdb=" N1 A1AB5 C1402 " ideal model delta sigma weight residual 1.275 1.452 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" C3 A1AB5 C1402 " pdb=" N2 A1AB5 C1402 " ideal model delta sigma weight residual 1.290 1.445 -0.155 2.00e-02 2.50e+03 6.03e+01 ... (remaining 25706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.81: 34666 4.81 - 9.62: 64 9.62 - 14.43: 1 14.43 - 19.24: 2 19.24 - 24.05: 6 Bond angle restraints: 34739 Sorted by residual: angle pdb=" C4 A1AB5 C1402 " pdb=" C3 A1AB5 C1402 " pdb=" N2 A1AB5 C1402 " ideal model delta sigma weight residual 116.15 92.10 24.05 3.00e+00 1.11e-01 6.42e+01 angle pdb=" C4 A1AB5 A1402 " pdb=" C3 A1AB5 A1402 " pdb=" N2 A1AB5 A1402 " ideal model delta sigma weight residual 116.15 92.49 23.66 3.00e+00 1.11e-01 6.22e+01 angle pdb=" C10 A1AB5 C1402 " pdb=" C3 A1AB5 C1402 " pdb=" C4 A1AB5 C1402 " ideal model delta sigma weight residual 118.62 141.61 -22.99 3.00e+00 1.11e-01 5.87e+01 angle pdb=" C10 A1AB5 A1402 " pdb=" C3 A1AB5 A1402 " pdb=" C4 A1AB5 A1402 " ideal model delta sigma weight residual 118.62 140.62 -22.00 3.00e+00 1.11e-01 5.38e+01 angle pdb=" C4 A1AB5 A1401 " pdb=" C3 A1AB5 A1401 " pdb=" N2 A1AB5 A1401 " ideal model delta sigma weight residual 116.15 94.22 21.93 3.00e+00 1.11e-01 5.34e+01 ... (remaining 34734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.59: 14493 22.59 - 45.18: 718 45.18 - 67.77: 69 67.77 - 90.36: 24 90.36 - 112.95: 1 Dihedral angle restraints: 15305 sinusoidal: 6140 harmonic: 9165 Sorted by residual: dihedral pdb=" CA CYS C 773 " pdb=" C CYS C 773 " pdb=" N GLY C 774 " pdb=" CA GLY C 774 " ideal model delta harmonic sigma weight residual 180.00 67.05 112.95 0 5.00e+00 4.00e-02 5.10e+02 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual -86.00 -163.04 77.04 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 156.24 -63.24 1 1.00e+01 1.00e-02 5.28e+01 ... (remaining 15302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2616 0.043 - 0.086: 909 0.086 - 0.129: 257 0.129 - 0.172: 41 0.172 - 0.215: 7 Chirality restraints: 3830 Sorted by residual: chirality pdb=" CB VAL B 630 " pdb=" CA VAL B 630 " pdb=" CG1 VAL B 630 " pdb=" CG2 VAL B 630 " 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 ILE D 534 " pdb=" CA ILE D 534 " pdb=" CG1 ILE D 534 " pdb=" CG2 ILE D 534 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CG LEU D 498 " pdb=" CB LEU D 498 " pdb=" CD1 LEU D 498 " pdb=" CD2 LEU D 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 3827 not shown) Planarity restraints: 4395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 453 " 0.245 9.50e-02 1.11e+02 1.10e-01 7.40e+00 pdb=" NE ARG D 453 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 453 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG D 453 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 453 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 592 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO D 593 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 593 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 593 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO D 99 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.022 5.00e-02 4.00e+02 ... (remaining 4392 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 374 2.67 - 3.23: 24939 3.23 - 3.79: 39443 3.79 - 4.34: 53093 4.34 - 4.90: 87860 Nonbonded interactions: 205709 Sorted by model distance: nonbonded pdb=" OE1 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.113 3.040 nonbonded pdb=" OG1 THR B 480 " pdb=" OXT GLU B1301 " model vdw 2.148 3.040 nonbonded pdb=" OG1 THR D 38 " pdb=" OE1 GLU D 40 " model vdw 2.185 3.040 nonbonded pdb=" OG SER A 243 " pdb=" OE1 GLU A 362 " model vdw 2.185 3.040 nonbonded pdb=" NH1 ARG B 309 " pdb=" O ASN B 311 " model vdw 2.220 3.120 ... (remaining 205704 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 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = (chain 'B' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 1301)) selection = (chain 'C' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.830 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 : 0.008 0.180 25721 Z= 0.368 Angle : 0.731 24.045 34755 Z= 0.361 Chirality : 0.047 0.215 3830 Planarity : 0.004 0.110 4395 Dihedral : 12.946 112.947 9429 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.63 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.15), residues: 3164 helix: 1.47 (0.14), residues: 1389 sheet: -0.62 (0.26), residues: 386 loop : -0.55 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 545 TYR 0.022 0.002 TYR A 702 PHE 0.022 0.002 PHE B 495 TRP 0.018 0.002 TRP B 323 HIS 0.009 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00797 (25711) covalent geometry : angle 0.73064 (34739) SS BOND : bond 0.00276 ( 8) SS BOND : angle 1.70180 ( 16) hydrogen bonds : bond 0.14293 ( 1198) hydrogen bonds : angle 5.89311 ( 3447) Misc. bond : bond 0.00438 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 705 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.6722 (m-30) cc_final: 0.6450 (t0) REVERT: A 371 ILE cc_start: 0.8051 (pt) cc_final: 0.7462 (tp) REVERT: A 767 TRP cc_start: 0.6723 (m-90) cc_final: 0.6516 (m-90) REVERT: B 23 ASP cc_start: 0.7238 (p0) cc_final: 0.7016 (m-30) REVERT: C 97 ILE cc_start: 0.6951 (mt) cc_final: 0.6496 (mt) REVERT: C 371 ILE cc_start: 0.7859 (pt) cc_final: 0.7529 (tp) REVERT: D 381 VAL cc_start: 0.6639 (t) cc_final: 0.6273 (t) REVERT: D 585 MET cc_start: 0.8884 (mmt) cc_final: 0.8359 (mmt) outliers start: 0 outliers final: 0 residues processed: 705 average time/residue: 0.2015 time to fit residues: 211.6369 Evaluate side-chains 329 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.174095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.134578 restraints weight = 54462.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.125851 restraints weight = 48358.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.126074 restraints weight = 30243.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.127017 restraints weight = 18436.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.126613 restraints weight = 15161.398| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25721 Z= 0.136 Angle : 0.597 9.722 34755 Z= 0.314 Chirality : 0.044 0.306 3830 Planarity : 0.004 0.069 4395 Dihedral : 4.634 49.500 3519 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.51 % Favored : 96.33 % Rotamer: Outliers : 1.73 % Allowed : 10.31 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.15), residues: 3164 helix: 1.69 (0.14), residues: 1427 sheet: -0.31 (0.26), residues: 390 loop : -0.54 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 715 TYR 0.017 0.001 TYR A 702 PHE 0.029 0.002 PHE B 546 TRP 0.026 0.002 TRP A 130 HIS 0.005 0.001 HIS C 93 Details of bonding type rmsd covalent geometry : bond 0.00299 (25711) covalent geometry : angle 0.59467 (34739) SS BOND : bond 0.01083 ( 8) SS BOND : angle 2.40501 ( 16) hydrogen bonds : bond 0.03698 ( 1198) hydrogen bonds : angle 4.49245 ( 3447) Misc. bond : bond 0.00137 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 386 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 HIS cc_start: 0.5378 (m90) cc_final: 0.5076 (m90) REVERT: A 231 ASP cc_start: 0.7467 (m-30) cc_final: 0.7121 (m-30) REVERT: A 402 GLU cc_start: 0.7199 (tp30) cc_final: 0.6965 (tp30) REVERT: A 407 MET cc_start: 0.7924 (mpp) cc_final: 0.7668 (mtm) REVERT: A 450 TYR cc_start: 0.7460 (m-80) cc_final: 0.6931 (m-80) REVERT: A 466 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 476 ILE cc_start: 0.7753 (mp) cc_final: 0.7391 (mp) REVERT: A 708 MET cc_start: 0.7965 (mtt) cc_final: 0.7379 (mtt) REVERT: A 715 ARG cc_start: 0.7753 (mmm160) cc_final: 0.7466 (mmp-170) REVERT: A 767 TRP cc_start: 0.7190 (m-90) cc_final: 0.6666 (m-90) REVERT: B 23 ASP cc_start: 0.7353 (p0) cc_final: 0.6863 (m-30) REVERT: B 292 MET cc_start: 0.7395 (tpp) cc_final: 0.5849 (ptm) REVERT: B 361 MET cc_start: 0.5212 (mtm) cc_final: 0.4611 (mtp) REVERT: B 738 LYS cc_start: 0.5588 (mmtm) cc_final: 0.5247 (mmtp) REVERT: C 642 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7670 (tm-30) REVERT: C 788 SER cc_start: 0.8808 (t) cc_final: 0.8563 (p) REVERT: D 106 THR cc_start: 0.7892 (m) cc_final: 0.7581 (p) REVERT: D 137 TYR cc_start: 0.7394 (p90) cc_final: 0.6780 (p90) REVERT: D 187 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8194 (tptt) REVERT: D 208 VAL cc_start: 0.8943 (t) cc_final: 0.8728 (t) REVERT: D 268 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7941 (tptm) REVERT: D 361 MET cc_start: 0.5447 (mmt) cc_final: 0.5209 (mmt) outliers start: 47 outliers final: 23 residues processed: 412 average time/residue: 0.1717 time to fit residues: 110.5150 Evaluate side-chains 284 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 261 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 592 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 64 optimal weight: 0.6980 chunk 314 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 188 optimal weight: 0.0170 chunk 191 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.173263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.133448 restraints weight = 53660.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.126879 restraints weight = 55523.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.126040 restraints weight = 43368.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.125736 restraints weight = 31261.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.126142 restraints weight = 27422.163| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25721 Z= 0.109 Angle : 0.542 8.125 34755 Z= 0.286 Chirality : 0.042 0.216 3830 Planarity : 0.004 0.064 4395 Dihedral : 4.310 42.879 3519 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.13 % Favored : 96.74 % Rotamer: Outliers : 1.84 % Allowed : 12.45 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.15), residues: 3164 helix: 1.92 (0.14), residues: 1429 sheet: -0.34 (0.25), residues: 403 loop : -0.58 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 660 TYR 0.012 0.001 TYR A 702 PHE 0.031 0.001 PHE B 296 TRP 0.022 0.001 TRP C 262 HIS 0.004 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00243 (25711) covalent geometry : angle 0.54126 (34739) SS BOND : bond 0.00324 ( 8) SS BOND : angle 1.68184 ( 16) hydrogen bonds : bond 0.03361 ( 1198) hydrogen bonds : angle 4.21267 ( 3447) Misc. bond : bond 0.00114 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 308 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.6695 (t80) cc_final: 0.6493 (t80) REVERT: A 231 ASP cc_start: 0.7471 (m-30) cc_final: 0.7173 (m-30) REVERT: A 402 GLU cc_start: 0.6987 (tp30) cc_final: 0.6734 (tp30) REVERT: A 708 MET cc_start: 0.7880 (mtt) cc_final: 0.7228 (mtt) REVERT: A 767 TRP cc_start: 0.7155 (m-90) cc_final: 0.6667 (m-90) REVERT: B 23 ASP cc_start: 0.7374 (p0) cc_final: 0.6667 (m-30) REVERT: B 292 MET cc_start: 0.7325 (tpp) cc_final: 0.5878 (ptm) REVERT: B 361 MET cc_start: 0.5381 (mtm) cc_final: 0.4970 (mtp) REVERT: C 97 ILE cc_start: 0.7557 (pt) cc_final: 0.7301 (mt) REVERT: C 767 TRP cc_start: 0.7780 (m-90) cc_final: 0.7328 (m-90) REVERT: D 18 PHE cc_start: 0.5340 (OUTLIER) cc_final: 0.4790 (m-10) REVERT: D 106 THR cc_start: 0.7757 (m) cc_final: 0.7444 (p) REVERT: D 137 TYR cc_start: 0.7224 (p90) cc_final: 0.6933 (p90) REVERT: D 268 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7907 (tptm) REVERT: D 381 VAL cc_start: 0.7120 (t) cc_final: 0.6915 (t) outliers start: 50 outliers final: 27 residues processed: 337 average time/residue: 0.1710 time to fit residues: 92.4186 Evaluate side-chains 281 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 136 optimal weight: 3.9990 chunk 302 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 288 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 246 optimal weight: 0.0770 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.169975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.129943 restraints weight = 52619.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.119687 restraints weight = 55361.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.120517 restraints weight = 34785.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.120457 restraints weight = 22207.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120236 restraints weight = 21648.152| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25721 Z= 0.150 Angle : 0.564 10.074 34755 Z= 0.295 Chirality : 0.043 0.175 3830 Planarity : 0.004 0.061 4395 Dihedral : 4.338 40.778 3519 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.98 % Favored : 95.89 % Rotamer: Outliers : 2.21 % Allowed : 13.04 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.15), residues: 3164 helix: 1.96 (0.14), residues: 1426 sheet: -0.48 (0.25), residues: 402 loop : -0.59 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 675 TYR 0.017 0.001 TYR A 270 PHE 0.029 0.002 PHE B 56 TRP 0.019 0.002 TRP C 262 HIS 0.005 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00348 (25711) covalent geometry : angle 0.56344 (34739) SS BOND : bond 0.00320 ( 8) SS BOND : angle 1.43288 ( 16) hydrogen bonds : bond 0.03658 ( 1198) hydrogen bonds : angle 4.16227 ( 3447) Misc. bond : bond 0.00205 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7870 (tpt170) REVERT: A 708 MET cc_start: 0.8030 (mtt) cc_final: 0.6996 (mtt) REVERT: A 767 TRP cc_start: 0.7271 (m-90) cc_final: 0.6867 (m-90) REVERT: B 23 ASP cc_start: 0.7340 (p0) cc_final: 0.6501 (m-30) REVERT: B 187 LYS cc_start: 0.7982 (tmtt) cc_final: 0.7600 (tptt) REVERT: B 292 MET cc_start: 0.6979 (tpp) cc_final: 0.5589 (ptm) REVERT: B 361 MET cc_start: 0.5573 (mtm) cc_final: 0.5216 (mtp) REVERT: C 767 TRP cc_start: 0.7789 (m-90) cc_final: 0.7516 (m-90) REVERT: D 106 THR cc_start: 0.7872 (m) cc_final: 0.7559 (p) REVERT: D 113 MET cc_start: 0.7472 (mpp) cc_final: 0.7198 (ptp) REVERT: D 137 TYR cc_start: 0.7378 (p90) cc_final: 0.6784 (p90) REVERT: D 268 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7927 (tptm) REVERT: D 292 MET cc_start: 0.7151 (mmm) cc_final: 0.5775 (ptm) REVERT: D 304 ILE cc_start: 0.3963 (mm) cc_final: 0.3697 (mt) outliers start: 60 outliers final: 37 residues processed: 320 average time/residue: 0.1691 time to fit residues: 87.4550 Evaluate side-chains 277 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 592 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 10.0000 chunk 270 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 268 optimal weight: 0.5980 chunk 228 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 231 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.167645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.127299 restraints weight = 52920.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.118317 restraints weight = 53197.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.119110 restraints weight = 35658.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.119068 restraints weight = 21944.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.119054 restraints weight = 22414.421| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25721 Z= 0.176 Angle : 0.587 13.233 34755 Z= 0.305 Chirality : 0.044 0.199 3830 Planarity : 0.004 0.047 4395 Dihedral : 4.417 35.073 3519 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 2.69 % Allowed : 14.00 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.15), residues: 3164 helix: 1.86 (0.14), residues: 1429 sheet: -0.51 (0.25), residues: 401 loop : -0.63 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 42 TYR 0.015 0.001 TYR B 77 PHE 0.029 0.002 PHE B 56 TRP 0.019 0.002 TRP C 374 HIS 0.006 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00418 (25711) covalent geometry : angle 0.58603 (34739) SS BOND : bond 0.00427 ( 8) SS BOND : angle 1.34556 ( 16) hydrogen bonds : bond 0.03759 ( 1198) hydrogen bonds : angle 4.16314 ( 3447) Misc. bond : bond 0.00261 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 258 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 THR cc_start: 0.7923 (p) cc_final: 0.7664 (t) REVERT: A 767 TRP cc_start: 0.7236 (m-90) cc_final: 0.6885 (m-90) REVERT: B 74 PHE cc_start: 0.6809 (OUTLIER) cc_final: 0.5926 (t80) REVERT: B 187 LYS cc_start: 0.8177 (tmtt) cc_final: 0.7616 (tptt) REVERT: B 361 MET cc_start: 0.5617 (mtm) cc_final: 0.5099 (mtp) REVERT: B 408 MET cc_start: 0.5853 (tmm) cc_final: 0.5367 (tmm) REVERT: B 738 LYS cc_start: 0.5129 (mmtm) cc_final: 0.4380 (ptmt) REVERT: C 500 ILE cc_start: 0.9320 (mm) cc_final: 0.8991 (mm) REVERT: C 788 SER cc_start: 0.9002 (t) cc_final: 0.8520 (m) REVERT: D 106 THR cc_start: 0.7896 (m) cc_final: 0.7618 (p) REVERT: D 137 TYR cc_start: 0.7376 (p90) cc_final: 0.6818 (p90) REVERT: D 268 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7930 (tptm) outliers start: 73 outliers final: 47 residues processed: 309 average time/residue: 0.1754 time to fit residues: 88.6044 Evaluate side-chains 271 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 229 optimal weight: 0.0570 chunk 253 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 305 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.168004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.131215 restraints weight = 54440.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.127288 restraints weight = 70509.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.126709 restraints weight = 52034.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.126536 restraints weight = 43007.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.125881 restraints weight = 37771.117| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25721 Z= 0.166 Angle : 0.578 12.054 34755 Z= 0.299 Chirality : 0.043 0.153 3830 Planarity : 0.004 0.045 4395 Dihedral : 4.382 36.046 3519 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 2.62 % Allowed : 15.51 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.15), residues: 3164 helix: 1.80 (0.14), residues: 1435 sheet: -0.54 (0.25), residues: 392 loop : -0.69 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 297 TYR 0.016 0.001 TYR B 280 PHE 0.030 0.002 PHE B 56 TRP 0.021 0.002 TRP A 262 HIS 0.009 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00397 (25711) covalent geometry : angle 0.57809 (34739) SS BOND : bond 0.00171 ( 8) SS BOND : angle 0.92568 ( 16) hydrogen bonds : bond 0.03668 ( 1198) hydrogen bonds : angle 4.14167 ( 3447) Misc. bond : bond 0.00246 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 245 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 THR cc_start: 0.7792 (p) cc_final: 0.7579 (t) REVERT: A 767 TRP cc_start: 0.7239 (m-90) cc_final: 0.6924 (m-90) REVERT: B 74 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.5706 (t80) REVERT: B 187 LYS cc_start: 0.8087 (tmtt) cc_final: 0.7804 (tmtt) REVERT: B 292 MET cc_start: 0.6996 (mmm) cc_final: 0.5723 (ptm) REVERT: B 361 MET cc_start: 0.5655 (mtm) cc_final: 0.5258 (mtp) REVERT: B 738 LYS cc_start: 0.4707 (mmtm) cc_final: 0.4185 (ptmt) REVERT: C 97 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6821 (pt) REVERT: C 673 TYR cc_start: 0.8621 (t80) cc_final: 0.8074 (t80) REVERT: C 788 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8546 (m) REVERT: D 18 PHE cc_start: 0.5391 (OUTLIER) cc_final: 0.4755 (m-10) REVERT: D 106 THR cc_start: 0.7907 (m) cc_final: 0.7605 (p) REVERT: D 137 TYR cc_start: 0.7255 (p90) cc_final: 0.6768 (p90) outliers start: 71 outliers final: 47 residues processed: 295 average time/residue: 0.1614 time to fit residues: 78.2026 Evaluate side-chains 269 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 286 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 301 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 289 optimal weight: 0.6980 chunk 293 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.168359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.128894 restraints weight = 54741.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.120086 restraints weight = 58228.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120285 restraints weight = 36677.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.120280 restraints weight = 25040.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120564 restraints weight = 26236.487| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25721 Z= 0.120 Angle : 0.550 11.406 34755 Z= 0.282 Chirality : 0.042 0.189 3830 Planarity : 0.003 0.042 4395 Dihedral : 4.168 32.517 3519 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.70 % Favored : 96.18 % Rotamer: Outliers : 2.36 % Allowed : 16.02 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.15), residues: 3164 helix: 1.96 (0.14), residues: 1428 sheet: -0.49 (0.26), residues: 379 loop : -0.67 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 42 TYR 0.018 0.001 TYR B 280 PHE 0.021 0.001 PHE B 56 TRP 0.023 0.001 TRP A 262 HIS 0.011 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00279 (25711) covalent geometry : angle 0.54961 (34739) SS BOND : bond 0.00304 ( 8) SS BOND : angle 0.89245 ( 16) hydrogen bonds : bond 0.03335 ( 1198) hydrogen bonds : angle 4.01349 ( 3447) Misc. bond : bond 0.00148 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 255 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 767 TRP cc_start: 0.7446 (m-90) cc_final: 0.7090 (m-90) REVERT: B 74 PHE cc_start: 0.6777 (OUTLIER) cc_final: 0.5892 (t80) REVERT: B 187 LYS cc_start: 0.8242 (tmtt) cc_final: 0.7960 (tmtt) REVERT: B 292 MET cc_start: 0.6901 (mmm) cc_final: 0.5655 (ptm) REVERT: B 361 MET cc_start: 0.5725 (mtm) cc_final: 0.5303 (mtp) REVERT: B 738 LYS cc_start: 0.4743 (mmtm) cc_final: 0.4271 (ptmt) REVERT: C 97 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6965 (pt) REVERT: C 407 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7005 (mpp) REVERT: C 670 MET cc_start: 0.8883 (mtp) cc_final: 0.8478 (mtp) REVERT: C 673 TYR cc_start: 0.8692 (t80) cc_final: 0.8152 (t80) REVERT: C 788 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8507 (m) REVERT: D 18 PHE cc_start: 0.5761 (OUTLIER) cc_final: 0.5189 (m-10) REVERT: D 106 THR cc_start: 0.8002 (m) cc_final: 0.7705 (p) REVERT: D 137 TYR cc_start: 0.7338 (p90) cc_final: 0.6747 (p90) outliers start: 64 outliers final: 45 residues processed: 299 average time/residue: 0.1583 time to fit residues: 78.5610 Evaluate side-chains 275 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 425 CYS Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 299 optimal weight: 5.9990 chunk 307 optimal weight: 20.0000 chunk 220 optimal weight: 6.9990 chunk 214 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 216 optimal weight: 0.5980 chunk 174 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.167294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.123713 restraints weight = 54239.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.115978 restraints weight = 53390.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.113492 restraints weight = 36346.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114177 restraints weight = 24811.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114140 restraints weight = 21808.452| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25721 Z= 0.143 Angle : 0.577 11.502 34755 Z= 0.293 Chirality : 0.043 0.197 3830 Planarity : 0.004 0.043 4395 Dihedral : 4.187 30.425 3519 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.39 % Rotamer: Outliers : 2.17 % Allowed : 16.94 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.15), residues: 3164 helix: 1.92 (0.14), residues: 1430 sheet: -0.52 (0.26), residues: 374 loop : -0.71 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 303 TYR 0.016 0.001 TYR B 280 PHE 0.037 0.001 PHE B 56 TRP 0.025 0.002 TRP A 262 HIS 0.012 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00340 (25711) covalent geometry : angle 0.57641 (34739) SS BOND : bond 0.00347 ( 8) SS BOND : angle 0.91493 ( 16) hydrogen bonds : bond 0.03565 ( 1198) hydrogen bonds : angle 4.04019 ( 3447) Misc. bond : bond 0.00199 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LYS cc_start: 0.6681 (pttm) cc_final: 0.6278 (tptp) REVERT: A 767 TRP cc_start: 0.7565 (m-90) cc_final: 0.7315 (m-90) REVERT: B 74 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6096 (t80) REVERT: B 93 HIS cc_start: 0.6110 (m-70) cc_final: 0.5567 (m170) REVERT: B 187 LYS cc_start: 0.8222 (tmtt) cc_final: 0.7947 (tmtt) REVERT: B 292 MET cc_start: 0.7010 (mmm) cc_final: 0.5626 (ptm) REVERT: B 361 MET cc_start: 0.5681 (mtm) cc_final: 0.5283 (mtp) REVERT: B 738 LYS cc_start: 0.5229 (mmtm) cc_final: 0.4655 (ptmt) REVERT: C 97 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7174 (pt) REVERT: C 407 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7335 (mpp) REVERT: C 673 TYR cc_start: 0.8804 (t80) cc_final: 0.8136 (t80) REVERT: C 681 VAL cc_start: 0.7907 (m) cc_final: 0.7698 (m) REVERT: C 788 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8564 (m) REVERT: D 18 PHE cc_start: 0.6186 (OUTLIER) cc_final: 0.5487 (m-10) REVERT: D 93 HIS cc_start: 0.6152 (m-70) cc_final: 0.5872 (m170) REVERT: D 106 THR cc_start: 0.8138 (m) cc_final: 0.7865 (p) REVERT: D 137 TYR cc_start: 0.7479 (p90) cc_final: 0.6711 (p90) outliers start: 59 outliers final: 44 residues processed: 284 average time/residue: 0.1674 time to fit residues: 77.0903 Evaluate side-chains 271 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 301 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.166335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.124835 restraints weight = 53149.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.114202 restraints weight = 55941.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115655 restraints weight = 33181.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.115051 restraints weight = 21491.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.114958 restraints weight = 24244.599| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25721 Z= 0.171 Angle : 0.600 13.439 34755 Z= 0.306 Chirality : 0.043 0.187 3830 Planarity : 0.004 0.043 4395 Dihedral : 4.310 30.870 3519 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.20 % Rotamer: Outliers : 2.17 % Allowed : 17.35 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.15), residues: 3164 helix: 1.80 (0.14), residues: 1439 sheet: -0.58 (0.26), residues: 374 loop : -0.77 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 369 TYR 0.018 0.001 TYR D 218 PHE 0.040 0.002 PHE B 56 TRP 0.025 0.002 TRP A 262 HIS 0.012 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00409 (25711) covalent geometry : angle 0.59976 (34739) SS BOND : bond 0.00166 ( 8) SS BOND : angle 0.95142 ( 16) hydrogen bonds : bond 0.03730 ( 1198) hydrogen bonds : angle 4.11954 ( 3447) Misc. bond : bond 0.00251 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.2220 (p90) cc_final: 0.1928 (p90) REVERT: A 407 MET cc_start: 0.7601 (mpp) cc_final: 0.7225 (mmt) REVERT: A 410 LYS cc_start: 0.6622 (pttm) cc_final: 0.6218 (tmtt) REVERT: A 767 TRP cc_start: 0.7585 (m-90) cc_final: 0.7376 (m-90) REVERT: B 74 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6067 (t80) REVERT: B 361 MET cc_start: 0.5799 (mtm) cc_final: 0.5429 (mtp) REVERT: B 738 LYS cc_start: 0.5093 (mmtm) cc_final: 0.4607 (ptmt) REVERT: C 97 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.7072 (pt) REVERT: C 316 LEU cc_start: 0.3256 (mt) cc_final: 0.2797 (pp) REVERT: C 407 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7356 (mpp) REVERT: C 673 TYR cc_start: 0.8748 (t80) cc_final: 0.8400 (t80) REVERT: C 788 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8623 (m) REVERT: D 18 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5470 (m-10) REVERT: D 106 THR cc_start: 0.8216 (m) cc_final: 0.7953 (p) REVERT: D 137 TYR cc_start: 0.7547 (p90) cc_final: 0.7293 (p90) outliers start: 59 outliers final: 46 residues processed: 279 average time/residue: 0.1616 time to fit residues: 74.7103 Evaluate side-chains 273 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 156 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 219 optimal weight: 0.0570 chunk 220 optimal weight: 0.9990 chunk 243 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.168703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.126887 restraints weight = 54566.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.118475 restraints weight = 51963.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.117819 restraints weight = 37481.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.117952 restraints weight = 27342.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.118024 restraints weight = 23370.228| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25721 Z= 0.110 Angle : 0.587 13.406 34755 Z= 0.296 Chirality : 0.042 0.193 3830 Planarity : 0.004 0.047 4395 Dihedral : 4.088 28.526 3519 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.11 % Favored : 95.76 % Rotamer: Outliers : 1.47 % Allowed : 18.53 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.15), residues: 3164 helix: 1.94 (0.14), residues: 1437 sheet: -0.49 (0.27), residues: 367 loop : -0.77 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 369 TYR 0.020 0.001 TYR C 26 PHE 0.045 0.001 PHE B 56 TRP 0.027 0.002 TRP A 262 HIS 0.012 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00250 (25711) covalent geometry : angle 0.58483 (34739) SS BOND : bond 0.00434 ( 8) SS BOND : angle 2.46860 ( 16) hydrogen bonds : bond 0.03248 ( 1198) hydrogen bonds : angle 4.00030 ( 3447) Misc. bond : bond 0.00101 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 259 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.2469 (p90) cc_final: 0.2167 (p90) REVERT: A 131 ASP cc_start: 0.8312 (m-30) cc_final: 0.8111 (p0) REVERT: A 410 LYS cc_start: 0.6549 (pttm) cc_final: 0.6209 (tmtt) REVERT: A 767 TRP cc_start: 0.7630 (m-90) cc_final: 0.7351 (m-90) REVERT: B 74 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6051 (t80) REVERT: B 93 HIS cc_start: 0.5819 (m-70) cc_final: 0.5610 (m-70) REVERT: B 231 ASP cc_start: 0.7799 (t0) cc_final: 0.7417 (p0) REVERT: B 292 MET cc_start: 0.6894 (mmm) cc_final: 0.5513 (ptm) REVERT: B 361 MET cc_start: 0.5728 (mtm) cc_final: 0.5344 (mtp) REVERT: B 738 LYS cc_start: 0.5072 (mmtm) cc_final: 0.4557 (ptmt) REVERT: C 97 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.7078 (pt) REVERT: C 316 LEU cc_start: 0.3950 (mt) cc_final: 0.3660 (pp) REVERT: C 407 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7231 (mpp) REVERT: C 500 ILE cc_start: 0.9312 (mm) cc_final: 0.8957 (mm) REVERT: C 673 TYR cc_start: 0.8743 (t80) cc_final: 0.8388 (t80) REVERT: C 788 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8554 (m) REVERT: D 18 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.5336 (m-10) REVERT: D 106 THR cc_start: 0.8164 (m) cc_final: 0.7887 (p) REVERT: D 137 TYR cc_start: 0.7431 (p90) cc_final: 0.6706 (p90) REVERT: D 292 MET cc_start: 0.7430 (mmm) cc_final: 0.5851 (ptt) REVERT: D 765 LYS cc_start: 0.6594 (tmtt) cc_final: 0.5712 (pttt) outliers start: 40 outliers final: 33 residues processed: 286 average time/residue: 0.1696 time to fit residues: 79.4628 Evaluate side-chains 269 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 276 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 206 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.163668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.122168 restraints weight = 54496.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.118562 restraints weight = 59254.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.114323 restraints weight = 39944.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.114870 restraints weight = 35455.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.114837 restraints weight = 25580.329| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.6199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 25721 Z= 0.281 Angle : 0.720 12.305 34755 Z= 0.370 Chirality : 0.047 0.207 3830 Planarity : 0.005 0.050 4395 Dihedral : 4.795 31.507 3519 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.72 % Favored : 94.15 % Rotamer: Outliers : 1.92 % Allowed : 18.27 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.15), residues: 3164 helix: 1.50 (0.14), residues: 1439 sheet: -0.88 (0.26), residues: 394 loop : -0.91 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 369 TYR 0.018 0.002 TYR D 218 PHE 0.040 0.002 PHE B 56 TRP 0.038 0.002 TRP B 130 HIS 0.012 0.001 HIS D 412 Details of bonding type rmsd covalent geometry : bond 0.00674 (25711) covalent geometry : angle 0.71834 (34739) SS BOND : bond 0.00376 ( 8) SS BOND : angle 2.17250 ( 16) hydrogen bonds : bond 0.04449 ( 1198) hydrogen bonds : angle 4.36911 ( 3447) Misc. bond : bond 0.00426 ( 2) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 5068.87 seconds wall clock time: 87 minutes 48.68 seconds (5268.68 seconds total)