Starting phenix.real_space_refine on Sat Jun 21 17:11:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vj6_43275/06_2025/8vj6_43275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vj6_43275/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vj6_43275/06_2025/8vj6_43275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vj6_43275/06_2025/8vj6_43275.map" model { file = "/net/cci-nas-00/data/ceres_data/8vj6_43275/06_2025/8vj6_43275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vj6_43275/06_2025/8vj6_43275.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.78, per 1000 atoms: 0.55 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: 5.90 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 3.31 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: 9.54 Time building geometry restraints manager: 6.91 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: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 55.610 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.100 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (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 TRP 0.018 0.002 TRP B 323 HIS 0.009 0.001 HIS B 214 PHE 0.022 0.002 PHE B 495 TYR 0.022 0.002 TYR A 702 ARG 0.006 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.14293 ( 1198) hydrogen bonds : angle 5.89311 ( 3447) SS BOND : bond 0.00276 ( 8) SS BOND : angle 1.70180 ( 16) covalent geometry : bond 0.00797 (25711) covalent geometry : angle 0.73064 (34739) 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 : 2.891 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: 0.4307 time to fit residues: 452.2223 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 : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 286 optimal weight: 7.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.166835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.124758 restraints weight = 52913.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.119468 restraints weight = 57987.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.116299 restraints weight = 43390.898| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 25721 Z= 0.283 Angle : 0.718 9.976 34755 Z= 0.380 Chirality : 0.048 0.245 3830 Planarity : 0.005 0.074 4395 Dihedral : 5.252 52.788 3519 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 2.65 % Allowed : 10.72 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3164 helix: 1.29 (0.14), residues: 1434 sheet: -0.66 (0.24), residues: 405 loop : -0.66 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 323 HIS 0.004 0.001 HIS C 93 PHE 0.029 0.002 PHE B 546 TYR 0.018 0.002 TYR D 77 ARG 0.008 0.001 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.04653 ( 1198) hydrogen bonds : angle 4.73390 ( 3447) SS BOND : bond 0.00825 ( 8) SS BOND : angle 2.23779 ( 16) covalent geometry : bond 0.00662 (25711) covalent geometry : angle 0.71617 (34739) Misc. bond : bond 0.00405 ( 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 387 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 315 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.6425 (tpp) cc_final: 0.6180 (tpp) REVERT: A 410 LYS cc_start: 0.7104 (pttm) cc_final: 0.6815 (tptp) REVERT: A 466 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 476 ILE cc_start: 0.8080 (mp) cc_final: 0.7720 (mp) REVERT: A 671 TRP cc_start: 0.8720 (t-100) cc_final: 0.8518 (t-100) REVERT: A 673 TYR cc_start: 0.8571 (t80) cc_final: 0.8016 (t80) REVERT: A 715 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7633 (mmp-170) REVERT: B 23 ASP cc_start: 0.7315 (p0) cc_final: 0.6654 (m-30) REVERT: B 137 TYR cc_start: 0.7468 (p90) cc_final: 0.7106 (p90) REVERT: B 292 MET cc_start: 0.7614 (tpp) cc_final: 0.6003 (ptt) REVERT: B 361 MET cc_start: 0.5489 (mtm) cc_final: 0.4815 (mtp) REVERT: B 374 TRP cc_start: 0.6562 (t60) cc_final: 0.6280 (t60) REVERT: B 483 LEU cc_start: 0.8790 (tp) cc_final: 0.8549 (tt) REVERT: C 292 MET cc_start: 0.6242 (mmm) cc_final: 0.6012 (mmm) REVERT: C 748 LEU cc_start: 0.8569 (mp) cc_final: 0.8291 (mp) REVERT: C 784 THR cc_start: 0.8149 (p) cc_final: 0.7838 (t) REVERT: C 788 SER cc_start: 0.8854 (t) cc_final: 0.8638 (m) REVERT: D 268 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7971 (tptm) REVERT: D 361 MET cc_start: 0.5497 (mmt) cc_final: 0.5257 (mmt) outliers start: 72 outliers final: 44 residues processed: 365 average time/residue: 0.3634 time to fit residues: 209.2307 Evaluate side-chains 264 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 174 ASP 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 712 ILE Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain B residue 85 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 225 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 381 VAL 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 C residue 46 HIS 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 376 GLU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 196 CYS 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 514 VAL Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 723 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 0.0050 chunk 106 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 65 optimal weight: 0.0000 chunk 183 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 overall best weight: 0.5802 ------------------------------------------------------------------------------- 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 = 0.4419 r_free = 0.4419 target = 0.170756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.130250 restraints weight = 52571.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.123935 restraints weight = 55462.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121907 restraints weight = 38998.000| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25721 Z= 0.113 Angle : 0.554 10.672 34755 Z= 0.293 Chirality : 0.042 0.227 3830 Planarity : 0.004 0.054 4395 Dihedral : 4.545 43.530 3519 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.16 % Favored : 96.71 % Rotamer: Outliers : 1.73 % Allowed : 13.48 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3164 helix: 1.78 (0.14), residues: 1430 sheet: -0.47 (0.25), residues: 389 loop : -0.61 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 262 HIS 0.004 0.001 HIS D 412 PHE 0.027 0.001 PHE B 546 TYR 0.015 0.001 TYR A 702 ARG 0.007 0.000 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 1198) hydrogen bonds : angle 4.23796 ( 3447) SS BOND : bond 0.00320 ( 8) SS BOND : angle 1.71234 ( 16) covalent geometry : bond 0.00250 (25711) covalent geometry : angle 0.55308 (34739) Misc. bond : bond 0.00108 ( 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 340 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 293 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 673 TYR cc_start: 0.8589 (t80) cc_final: 0.8217 (t80) REVERT: A 767 TRP cc_start: 0.7248 (m-90) cc_final: 0.6707 (m-90) REVERT: B 292 MET cc_start: 0.7196 (tpp) cc_final: 0.5670 (ptm) REVERT: B 361 MET cc_start: 0.5546 (mtm) cc_final: 0.3914 (mtt) REVERT: B 374 TRP cc_start: 0.6441 (t60) cc_final: 0.5911 (t60) REVERT: C 292 MET cc_start: 0.6132 (mmm) cc_final: 0.5656 (mmm) REVERT: C 644 GLU cc_start: 0.7670 (tp30) cc_final: 0.7452 (tp30) REVERT: C 784 THR cc_start: 0.8063 (p) cc_final: 0.7775 (t) REVERT: C 788 SER cc_start: 0.8927 (t) cc_final: 0.8577 (m) REVERT: D 18 PHE cc_start: 0.6119 (OUTLIER) cc_final: 0.5760 (m-10) REVERT: D 137 TYR cc_start: 0.7267 (p90) cc_final: 0.6911 (p90) REVERT: D 268 LYS cc_start: 0.8371 (mtpt) cc_final: 0.7948 (tptm) outliers start: 47 outliers final: 26 residues processed: 318 average time/residue: 0.3581 time to fit residues: 183.3067 Evaluate side-chains 264 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 381 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain B residue 85 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 585 MET Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 712 ILE 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 341 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 807 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 19 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 294 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 overall best weight: 3.2586 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.165220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.123306 restraints weight = 54451.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.119692 restraints weight = 65357.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.117803 restraints weight = 40768.806| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 25721 Z= 0.251 Angle : 0.649 8.573 34755 Z= 0.343 Chirality : 0.045 0.189 3830 Planarity : 0.004 0.051 4395 Dihedral : 4.958 39.840 3519 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.61 % Favored : 95.26 % Rotamer: Outliers : 2.98 % Allowed : 14.73 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3164 helix: 1.44 (0.14), residues: 1446 sheet: -0.63 (0.25), residues: 389 loop : -0.77 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 323 HIS 0.005 0.001 HIS B 46 PHE 0.028 0.002 PHE B 296 TYR 0.022 0.002 TYR B 77 ARG 0.006 0.001 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 1198) hydrogen bonds : angle 4.45436 ( 3447) SS BOND : bond 0.00552 ( 8) SS BOND : angle 1.83187 ( 16) covalent geometry : bond 0.00600 (25711) covalent geometry : angle 0.64807 (34739) Misc. bond : bond 0.00383 ( 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 322 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 241 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8699 (mm) REVERT: B 361 MET cc_start: 0.5664 (mtm) cc_final: 0.5256 (mtp) REVERT: B 643 THR cc_start: 0.8623 (p) cc_final: 0.8331 (t) REVERT: B 765 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6588 (ptmm) REVERT: C 116 ASP cc_start: 0.7719 (t0) cc_final: 0.7438 (p0) REVERT: C 292 MET cc_start: 0.5598 (mmm) cc_final: 0.5353 (mmm) REVERT: C 370 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7657 (tmtt) REVERT: C 407 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7150 (mpp) REVERT: C 784 THR cc_start: 0.8298 (p) cc_final: 0.7940 (t) REVERT: C 788 SER cc_start: 0.9093 (t) cc_final: 0.8842 (m) REVERT: D 18 PHE cc_start: 0.6144 (OUTLIER) cc_final: 0.5641 (m-10) REVERT: D 137 TYR cc_start: 0.7514 (p90) cc_final: 0.7299 (p90) REVERT: D 304 ILE cc_start: 0.4319 (mm) cc_final: 0.4071 (mt) REVERT: D 782 GLU cc_start: 0.6482 (mp0) cc_final: 0.6152 (tt0) outliers start: 81 outliers final: 53 residues processed: 298 average time/residue: 0.3578 time to fit residues: 170.6187 Evaluate side-chains 269 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 211 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 274 HIS 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 A residue 773 CYS Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain B residue 31 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 248 VAL 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 454 ASP 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 585 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 73 ILE 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 354 ILE Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 183 ASP 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 402 GLU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 589 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 174 optimal weight: 10.0000 chunk 217 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 chunk 251 optimal weight: 4.9990 chunk 283 optimal weight: 8.9990 chunk 313 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.168196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.126626 restraints weight = 52857.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.116746 restraints weight = 54383.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.116985 restraints weight = 35822.942| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5055 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= 0.123 Angle : 0.543 8.349 34755 Z= 0.286 Chirality : 0.042 0.167 3830 Planarity : 0.004 0.045 4395 Dihedral : 4.474 39.000 3519 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.82 % Favored : 96.05 % Rotamer: Outliers : 2.03 % Allowed : 16.32 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3164 helix: 1.78 (0.14), residues: 1443 sheet: -0.54 (0.26), residues: 385 loop : -0.76 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 374 HIS 0.010 0.001 HIS D 412 PHE 0.028 0.001 PHE B 56 TYR 0.019 0.001 TYR D 127 ARG 0.005 0.000 ARG C 30 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 1198) hydrogen bonds : angle 4.12137 ( 3447) SS BOND : bond 0.00289 ( 8) SS BOND : angle 1.27391 ( 16) covalent geometry : bond 0.00283 (25711) covalent geometry : angle 0.54282 (34739) Misc. bond : bond 0.00157 ( 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 312 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 257 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8361 (m-30) cc_final: 0.8052 (p0) REVERT: A 184 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8669 (mm) REVERT: A 767 TRP cc_start: 0.7253 (m-90) cc_final: 0.6774 (m-90) REVERT: B 292 MET cc_start: 0.6886 (mmm) cc_final: 0.5510 (ptm) REVERT: B 361 MET cc_start: 0.5674 (mtm) cc_final: 0.5297 (mtp) REVERT: B 485 ARG cc_start: 0.5373 (mtp85) cc_final: 0.4994 (ptm160) REVERT: B 643 THR cc_start: 0.8667 (p) cc_final: 0.8372 (t) REVERT: C 269 GLU cc_start: 0.6272 (pm20) cc_final: 0.5884 (tp30) REVERT: C 370 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7423 (tmtt) REVERT: C 407 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7255 (mpp) REVERT: C 585 MET cc_start: 0.8959 (mmt) cc_final: 0.8584 (mmt) REVERT: C 784 THR cc_start: 0.8185 (p) cc_final: 0.7820 (t) REVERT: C 788 SER cc_start: 0.8958 (t) cc_final: 0.8662 (m) REVERT: D 18 PHE cc_start: 0.6291 (OUTLIER) cc_final: 0.5599 (m-10) REVERT: D 137 TYR cc_start: 0.7413 (p90) cc_final: 0.6818 (p90) REVERT: D 292 MET cc_start: 0.7399 (mmm) cc_final: 0.5784 (ptm) REVERT: D 304 ILE cc_start: 0.3987 (mm) cc_final: 0.3741 (mt) outliers start: 55 outliers final: 37 residues processed: 296 average time/residue: 0.3430 time to fit residues: 165.3100 Evaluate side-chains 263 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 274 HIS 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 A residue 784 THR Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain B residue 84 THR 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 274 HIS 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 597 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 141 ARG 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 589 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 82 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 300 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 255 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.165579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.124303 restraints weight = 52707.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.117053 restraints weight = 56787.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.116157 restraints weight = 39905.686| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25721 Z= 0.207 Angle : 0.606 12.647 34755 Z= 0.316 Chirality : 0.044 0.183 3830 Planarity : 0.004 0.049 4395 Dihedral : 4.681 38.829 3519 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.99 % Favored : 94.88 % Rotamer: Outliers : 2.62 % Allowed : 16.54 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 3164 helix: 1.61 (0.14), residues: 1443 sheet: -0.79 (0.25), residues: 397 loop : -0.80 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 374 HIS 0.011 0.001 HIS D 412 PHE 0.029 0.002 PHE B 56 TYR 0.017 0.001 TYR B 77 ARG 0.007 0.001 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1198) hydrogen bonds : angle 4.26249 ( 3447) SS BOND : bond 0.00625 ( 8) SS BOND : angle 1.14651 ( 16) covalent geometry : bond 0.00494 (25711) covalent geometry : angle 0.60592 (34739) Misc. bond : bond 0.00319 ( 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 306 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 235 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 361 MET cc_start: 0.5717 (mtm) cc_final: 0.5406 (mtp) REVERT: B 480 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7343 (p) REVERT: B 765 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6640 (ptmm) REVERT: C 116 ASP cc_start: 0.7615 (t0) cc_final: 0.7358 (p0) REVERT: C 269 GLU cc_start: 0.6499 (pm20) cc_final: 0.6014 (tp30) REVERT: C 370 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7546 (tmtt) REVERT: C 407 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7303 (mpp) REVERT: C 585 MET cc_start: 0.8963 (mmt) cc_final: 0.8711 (mmt) REVERT: C 784 THR cc_start: 0.8193 (p) cc_final: 0.7776 (t) REVERT: C 788 SER cc_start: 0.9068 (t) cc_final: 0.8798 (m) REVERT: D 18 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.5703 (m-10) REVERT: D 137 TYR cc_start: 0.7531 (p90) cc_final: 0.7310 (p90) REVERT: D 304 ILE cc_start: 0.4112 (mm) cc_final: 0.3855 (mt) REVERT: D 782 GLU cc_start: 0.6577 (mp0) cc_final: 0.6224 (tt0) outliers start: 71 outliers final: 54 residues processed: 287 average time/residue: 0.3565 time to fit residues: 166.6409 Evaluate side-chains 271 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 274 HIS 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 773 CYS Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 84 THR 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 476 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 46 HIS 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 354 ILE Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 753 LEU 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 141 ARG 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 166 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 202 optimal weight: 0.7980 chunk 219 optimal weight: 0.0020 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 chunk 246 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- 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 = 0.4379 r_free = 0.4379 target = 0.167803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.126153 restraints weight = 52838.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.119520 restraints weight = 52283.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.118240 restraints weight = 43094.153| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5553 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= 0.120 Angle : 0.543 13.486 34755 Z= 0.280 Chirality : 0.042 0.164 3830 Planarity : 0.004 0.044 4395 Dihedral : 4.340 37.112 3519 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.98 % Favored : 95.89 % Rotamer: Outliers : 2.69 % Allowed : 17.02 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 3164 helix: 1.87 (0.14), residues: 1434 sheet: -0.67 (0.26), residues: 394 loop : -0.80 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 374 HIS 0.012 0.001 HIS D 412 PHE 0.028 0.001 PHE A 658 TYR 0.019 0.001 TYR C 26 ARG 0.006 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 1198) hydrogen bonds : angle 4.03196 ( 3447) SS BOND : bond 0.00220 ( 8) SS BOND : angle 0.96562 ( 16) covalent geometry : bond 0.00277 (25711) covalent geometry : angle 0.54227 (34739) Misc. bond : bond 0.00153 ( 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 338 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 265 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8634 (mm) REVERT: A 247 ILE cc_start: 0.8285 (tp) cc_final: 0.8010 (tt) REVERT: A 767 TRP cc_start: 0.7362 (m-90) cc_final: 0.6996 (m-90) REVERT: B 292 MET cc_start: 0.6853 (mmm) cc_final: 0.5519 (ptm) REVERT: B 361 MET cc_start: 0.5630 (mtm) cc_final: 0.5402 (mtp) REVERT: B 374 TRP cc_start: 0.6058 (t60) cc_final: 0.5847 (t60) REVERT: C 41 PHE cc_start: 0.3161 (p90) cc_final: 0.2843 (p90) REVERT: C 269 GLU cc_start: 0.6472 (pm20) cc_final: 0.6037 (tp30) REVERT: C 370 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7533 (tmtt) REVERT: C 407 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7263 (mpp) REVERT: C 585 MET cc_start: 0.8964 (mmt) cc_final: 0.8645 (mmt) REVERT: C 673 TYR cc_start: 0.8665 (t80) cc_final: 0.8217 (t80) REVERT: C 784 THR cc_start: 0.8139 (p) cc_final: 0.7746 (t) REVERT: C 788 SER cc_start: 0.8955 (t) cc_final: 0.8669 (m) REVERT: D 18 PHE cc_start: 0.6061 (OUTLIER) cc_final: 0.5233 (m-10) REVERT: D 137 TYR cc_start: 0.7360 (p90) cc_final: 0.6740 (p90) REVERT: D 292 MET cc_start: 0.7076 (mmm) cc_final: 0.5585 (ptm) REVERT: D 304 ILE cc_start: 0.3933 (mm) cc_final: 0.3656 (mt) REVERT: D 700 TYR cc_start: 0.7366 (t80) cc_final: 0.7150 (t80) REVERT: D 782 GLU cc_start: 0.6425 (mp0) cc_final: 0.6185 (tt0) outliers start: 73 outliers final: 52 residues processed: 320 average time/residue: 0.3563 time to fit residues: 183.6957 Evaluate side-chains 289 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 274 HIS 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 626 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 84 THR 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 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 C residue 44 THR 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 370 LYS Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 773 CYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 157 optimal weight: 1.9990 chunk 239 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 258 optimal weight: 0.6980 chunk 299 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.163924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122619 restraints weight = 52528.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.117320 restraints weight = 57766.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.115564 restraints weight = 37177.914| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 25721 Z= 0.253 Angle : 0.659 15.744 34755 Z= 0.342 Chirality : 0.045 0.180 3830 Planarity : 0.004 0.049 4395 Dihedral : 4.849 37.127 3519 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.44 % Favored : 94.44 % Rotamer: Outliers : 2.65 % Allowed : 17.35 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3164 helix: 1.49 (0.14), residues: 1435 sheet: -0.87 (0.26), residues: 400 loop : -0.96 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 374 HIS 0.012 0.001 HIS D 412 PHE 0.028 0.002 PHE A 658 TYR 0.019 0.002 TYR B 77 ARG 0.007 0.001 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 1198) hydrogen bonds : angle 4.33129 ( 3447) SS BOND : bond 0.00223 ( 8) SS BOND : angle 1.07011 ( 16) covalent geometry : bond 0.00608 (25711) covalent geometry : angle 0.65915 (34739) Misc. bond : bond 0.00385 ( 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 301 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 229 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ILE cc_start: 0.8197 (tp) cc_final: 0.7919 (tt) REVERT: B 187 LYS cc_start: 0.8257 (tmtt) cc_final: 0.7838 (tptt) REVERT: B 361 MET cc_start: 0.5854 (mtm) cc_final: 0.5590 (mtp) REVERT: C 269 GLU cc_start: 0.6467 (pm20) cc_final: 0.5932 (tp30) REVERT: C 370 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7552 (tmtt) REVERT: C 407 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7182 (mpp) REVERT: C 784 THR cc_start: 0.8174 (p) cc_final: 0.7718 (t) REVERT: C 788 SER cc_start: 0.9109 (t) cc_final: 0.8881 (m) REVERT: D 18 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.5447 (m-10) REVERT: D 74 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.5835 (t80) REVERT: D 268 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7879 (tptm) REVERT: D 304 ILE cc_start: 0.4073 (mm) cc_final: 0.3780 (mt) REVERT: D 782 GLU cc_start: 0.6431 (mp0) cc_final: 0.6098 (tt0) outliers start: 72 outliers final: 58 residues processed: 283 average time/residue: 0.3448 time to fit residues: 157.3544 Evaluate side-chains 264 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 202 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 274 HIS 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 626 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 84 THR 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 296 PHE Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 511 LYS 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 44 THR Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 74 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 284 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 481 ILE Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 683 VAL 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 172 optimal weight: 0.9990 chunk 249 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 214 optimal weight: 0.0270 chunk 97 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 283 optimal weight: 0.0020 overall best weight: 0.5246 ------------------------------------------------------------------------------- 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 = 0.168043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.127592 restraints weight = 52822.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119537 restraints weight = 53744.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.120062 restraints weight = 34577.971| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25721 Z= 0.108 Angle : 0.564 13.350 34755 Z= 0.289 Chirality : 0.042 0.176 3830 Planarity : 0.004 0.043 4395 Dihedral : 4.357 33.633 3519 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.95 % Rotamer: Outliers : 2.10 % Allowed : 18.05 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3164 helix: 1.81 (0.14), residues: 1441 sheet: -0.65 (0.27), residues: 375 loop : -0.88 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 374 HIS 0.016 0.001 HIS D 412 PHE 0.048 0.001 PHE B 56 TYR 0.020 0.001 TYR C 26 ARG 0.007 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 1198) hydrogen bonds : angle 4.03718 ( 3447) SS BOND : bond 0.00145 ( 8) SS BOND : angle 0.89776 ( 16) covalent geometry : bond 0.00239 (25711) covalent geometry : angle 0.56393 (34739) Misc. bond : bond 0.00100 ( 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 308 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 251 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ILE cc_start: 0.8198 (tp) cc_final: 0.7965 (tt) REVERT: A 362 GLU cc_start: 0.6916 (pm20) cc_final: 0.6688 (pm20) REVERT: A 767 TRP cc_start: 0.7434 (m-90) cc_final: 0.7106 (m-90) REVERT: B 187 LYS cc_start: 0.8189 (tmtt) cc_final: 0.7892 (tptt) REVERT: B 292 MET cc_start: 0.6792 (mmm) cc_final: 0.5482 (ptm) REVERT: C 269 GLU cc_start: 0.6307 (pm20) cc_final: 0.5900 (tp30) REVERT: C 370 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7519 (tmtt) REVERT: C 407 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7261 (mpp) REVERT: C 674 MET cc_start: 0.8371 (mtt) cc_final: 0.8058 (mtm) REVERT: C 784 THR cc_start: 0.8141 (p) cc_final: 0.7667 (t) REVERT: C 788 SER cc_start: 0.8970 (t) cc_final: 0.8686 (m) REVERT: D 18 PHE cc_start: 0.5949 (OUTLIER) cc_final: 0.5087 (m-10) REVERT: D 74 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6054 (t80) REVERT: D 137 TYR cc_start: 0.7389 (p90) cc_final: 0.6785 (p90) REVERT: D 292 MET cc_start: 0.7443 (mmm) cc_final: 0.5830 (ptm) REVERT: D 304 ILE cc_start: 0.3923 (mm) cc_final: 0.3604 (mt) REVERT: D 700 TYR cc_start: 0.7349 (t80) cc_final: 0.7099 (t80) REVERT: D 782 GLU cc_start: 0.6354 (mp0) cc_final: 0.6051 (tt0) outliers start: 57 outliers final: 46 residues processed: 288 average time/residue: 0.3445 time to fit residues: 159.4297 Evaluate side-chains 277 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 274 HIS 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 626 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain B residue 31 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 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 358 ILE Chi-restraints excluded: chain B residue 476 ILE 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 704 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 141 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 21 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 88 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 297 optimal weight: 0.7980 chunk 287 optimal weight: 1.9990 chunk 150 optimal weight: 0.0170 chunk 37 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- 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 = 0.167058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.123596 restraints weight = 52906.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.118726 restraints weight = 54941.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.116176 restraints weight = 34793.359| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.6058 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= 0.134 Angle : 0.590 13.672 34755 Z= 0.301 Chirality : 0.043 0.237 3830 Planarity : 0.004 0.045 4395 Dihedral : 4.345 32.422 3519 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.61 % Favored : 95.26 % Rotamer: Outliers : 1.92 % Allowed : 18.78 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3164 helix: 1.82 (0.14), residues: 1439 sheet: -0.67 (0.27), residues: 389 loop : -0.87 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 262 HIS 0.014 0.001 HIS D 412 PHE 0.040 0.001 PHE B 56 TYR 0.012 0.001 TYR C 673 ARG 0.007 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 1198) hydrogen bonds : angle 4.05464 ( 3447) SS BOND : bond 0.00137 ( 8) SS BOND : angle 0.91057 ( 16) covalent geometry : bond 0.00318 (25711) covalent geometry : angle 0.58945 (34739) Misc. bond : bond 0.00173 ( 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: 52 poor density : 247 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ILE cc_start: 0.8256 (tp) cc_final: 0.8039 (tt) REVERT: A 362 GLU cc_start: 0.7040 (pm20) cc_final: 0.6741 (pm20) REVERT: A 453 ARG cc_start: 0.8240 (tpp80) cc_final: 0.8028 (tpt170) REVERT: B 187 LYS cc_start: 0.8139 (tmtt) cc_final: 0.7827 (tptt) REVERT: C 97 ILE cc_start: 0.7557 (mm) cc_final: 0.7112 (pt) REVERT: C 269 GLU cc_start: 0.6375 (pm20) cc_final: 0.5931 (tp30) REVERT: C 316 LEU cc_start: 0.3370 (mt) cc_final: 0.2898 (pp) REVERT: C 370 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7382 (tmtt) REVERT: C 407 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7227 (mpp) REVERT: C 585 MET cc_start: 0.8964 (mmt) cc_final: 0.8627 (mmt) REVERT: C 784 THR cc_start: 0.8055 (p) cc_final: 0.7595 (t) REVERT: C 788 SER cc_start: 0.9011 (t) cc_final: 0.8727 (m) REVERT: D 18 PHE cc_start: 0.6222 (OUTLIER) cc_final: 0.5273 (m-10) REVERT: D 74 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6204 (t80) REVERT: D 137 TYR cc_start: 0.7412 (p90) cc_final: 0.6682 (p90) REVERT: D 292 MET cc_start: 0.7475 (mmm) cc_final: 0.5775 (ptm) REVERT: D 304 ILE cc_start: 0.3779 (mm) cc_final: 0.3468 (mt) REVERT: D 782 GLU cc_start: 0.6396 (mp0) cc_final: 0.6167 (tt0) outliers start: 52 outliers final: 44 residues processed: 279 average time/residue: 0.3384 time to fit residues: 153.6103 Evaluate side-chains 283 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 274 HIS 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 527 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain B residue 31 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 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 476 ILE 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 C residue 44 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 141 ARG 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 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 91 optimal weight: 0.9980 chunk 220 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.165385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.124764 restraints weight = 53041.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.116193 restraints weight = 58220.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.115557 restraints weight = 42983.363| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25721 Z= 0.195 Angle : 0.635 14.401 34755 Z= 0.325 Chirality : 0.044 0.185 3830 Planarity : 0.004 0.048 4395 Dihedral : 4.599 34.036 3519 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.37 % Favored : 94.50 % Rotamer: Outliers : 2.17 % Allowed : 18.53 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3164 helix: 1.64 (0.14), residues: 1435 sheet: -0.75 (0.27), residues: 389 loop : -0.94 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 262 HIS 0.014 0.001 HIS D 412 PHE 0.035 0.002 PHE B 56 TYR 0.013 0.001 TYR B 77 ARG 0.007 0.001 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 1198) hydrogen bonds : angle 4.19566 ( 3447) SS BOND : bond 0.00364 ( 8) SS BOND : angle 2.41162 ( 16) covalent geometry : bond 0.00469 (25711) covalent geometry : angle 0.63269 (34739) Misc. bond : bond 0.00296 ( 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: 9012.85 seconds wall clock time: 155 minutes 27.72 seconds (9327.72 seconds total)