Starting phenix.real_space_refine on Sat May 24 04:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vj6_43275/05_2025/8vj6_43275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vj6_43275/05_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_43275/05_2025/8vj6_43275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vj6_43275/05_2025/8vj6_43275.map" model { file = "/net/cci-nas-00/data/ceres_data/8vj6_43275/05_2025/8vj6_43275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vj6_43275/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 15.59, per 1000 atoms: 0.62 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: 6.74 Conformation dependent library (CDL) restraints added in 3.4 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: 3.51 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: 9.45 Time building geometry restraints manager: 7.76 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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 58.520 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.110 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.220 ------------------------------------------------------------------------------- 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 : 2.630 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: 0.4128 time to fit residues: 432.1986 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 : 2.731 ------------------------------------------------------------------------------- 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 = 52913.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.119470 restraints weight = 57986.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.116305 restraints weight = 43379.888| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- 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 : 2.828 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: 0.6179 (tpp) REVERT: A 410 LYS cc_start: 0.7103 (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: 0.7977 (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: 0.6002 (ptt) REVERT: B 361 MET cc_start: 0.5488 (mtm) cc_final: 0.4815 (mtp) REVERT: B 374 TRP cc_start: 0.6561 (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: 0.6013 (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: 0.8637 (m) REVERT: D 268 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7971 (tptm) REVERT: D 361 MET cc_start: 0.5498 (mmt) cc_final: 0.5258 (mmt) outliers start: 72 outliers final: 44 residues processed: 365 average time/residue: 0.3581 time to fit residues: 205.8512 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 : 2.802 ------------------------------------------------------------------------------- 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: 0.0030 chunk 106 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 65 optimal weight: 0.1980 chunk 183 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- 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 = 0.4409 r_free = 0.4409 target = 0.169950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.129221 restraints weight = 52684.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.123238 restraints weight = 56139.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.122002 restraints weight = 36685.798| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25721 Z= 0.119 Angle : 0.560 10.598 34755 Z= 0.297 Chirality : 0.043 0.213 3830 Planarity : 0.004 0.058 4395 Dihedral : 4.626 45.143 3519 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.54 % Favored : 96.33 % Rotamer: Outliers : 1.95 % Allowed : 13.26 % 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: 0.67 (0.15), residues: 3164 helix: 1.74 (0.14), residues: 1429 sheet: -0.57 (0.25), residues: 385 loop : -0.62 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 262 HIS 0.004 0.001 HIS D 412 PHE 0.028 0.001 PHE B 296 TYR 0.015 0.001 TYR A 702 ARG 0.007 0.000 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 1198) hydrogen bonds : angle 4.28167 ( 3447) SS BOND : bond 0.00261 ( 8) SS BOND : angle 1.97665 ( 16) covalent geometry : bond 0.00268 (25711) covalent geometry : angle 0.55850 (34739) Misc. bond : bond 0.00138 ( 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 334 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 281 time to evaluate : 2.562 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: 0.8568 (t80) cc_final: 0.8203 (t80) REVERT: A 767 TRP cc_start: 0.7254 (m-90) cc_final: 0.6677 (m-90) REVERT: B 137 TYR cc_start: 0.7381 (p90) cc_final: 0.7011 (p90) REVERT: B 292 MET cc_start: 0.7368 (tpp) cc_final: 0.5796 (ptm) REVERT: B 361 MET cc_start: 0.5606 (mtm) cc_final: 0.5176 (mtp) REVERT: B 374 TRP cc_start: 0.6364 (t60) cc_final: 0.5823 (t60) REVERT: C 292 MET cc_start: 0.6038 (mmm) cc_final: 0.5561 (mmm) REVERT: C 644 GLU cc_start: 0.7543 (tp30) cc_final: 0.7322 (tp30) REVERT: C 784 THR cc_start: 0.8087 (p) cc_final: 0.7763 (t) REVERT: C 788 SER cc_start: 0.9025 (t) cc_final: 0.8705 (m) REVERT: D 18 PHE cc_start: 0.5957 (OUTLIER) cc_final: 0.5653 (m-10) REVERT: D 137 TYR cc_start: 0.7234 (p90) cc_final: 0.6811 (p90) REVERT: D 141 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7673 (mtm110) REVERT: D 268 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7937 (tptm) outliers start: 53 outliers final: 31 residues processed: 312 average time/residue: 0.3341 time to fit residues: 167.1497 Evaluate side-chains 263 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 2.593 ------------------------------------------------------------------------------- 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 546 PHE Chi-restraints excluded: chain B residue 585 MET 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 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 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 399 THR Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 807 MET Rotamers are restrained with sigma=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: 0.8980 chunk 84 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 294 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- 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 = 0.4340 r_free = 0.4340 target = 0.164349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.122530 restraints weight = 53723.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.115438 restraints weight = 58374.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114025 restraints weight = 43551.695| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 25721 Z= 0.322 Angle : 0.707 12.991 34755 Z= 0.374 Chirality : 0.048 0.228 3830 Planarity : 0.005 0.061 4395 Dihedral : 5.299 42.484 3519 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.97 % Rotamer: Outliers : 3.28 % Allowed : 14.77 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.15 (0.15), residues: 3164 helix: 1.25 (0.14), residues: 1439 sheet: -0.79 (0.25), residues: 388 loop : -0.84 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 323 HIS 0.006 0.001 HIS B 46 PHE 0.033 0.003 PHE B 296 TYR 0.025 0.002 TYR B 77 ARG 0.007 0.001 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.04698 ( 1198) hydrogen bonds : angle 4.63029 ( 3447) SS BOND : bond 0.00243 ( 8) SS BOND : angle 1.86714 ( 16) covalent geometry : bond 0.00773 (25711) covalent geometry : angle 0.70554 (34739) Misc. bond : bond 0.00454 ( 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 327 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 238 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 361 MET cc_start: 0.5677 (mtm) cc_final: 0.5307 (mtp) REVERT: B 408 MET cc_start: 0.6128 (tmm) cc_final: 0.5758 (tmm) REVERT: B 546 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8420 (p90) REVERT: B 765 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6815 (ptmm) REVERT: C 116 ASP cc_start: 0.7758 (t0) cc_final: 0.7513 (p0) REVERT: C 292 MET cc_start: 0.5689 (mmm) cc_final: 0.5432 (mmm) REVERT: C 407 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7272 (mpp) REVERT: C 784 THR cc_start: 0.8198 (p) cc_final: 0.7768 (t) REVERT: C 807 MET cc_start: 0.8539 (mtm) cc_final: 0.8321 (mtm) REVERT: D 18 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.5850 (m-10) REVERT: D 268 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7870 (tptm) REVERT: D 304 ILE cc_start: 0.4366 (mm) cc_final: 0.4142 (mt) REVERT: D 782 GLU cc_start: 0.6570 (mp0) cc_final: 0.6221 (tt0) outliers start: 89 outliers final: 57 residues processed: 304 average time/residue: 0.3497 time to fit residues: 169.8813 Evaluate side-chains 264 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 203 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 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 546 PHE Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 765 LYS 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 289 VAL Chi-restraints excluded: chain C residue 354 ILE 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 503 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 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 481 ILE Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 617 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 174 optimal weight: 8.9990 chunk 217 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 251 optimal weight: 4.9990 chunk 283 optimal weight: 20.0000 chunk 313 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.168243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.126904 restraints weight = 52959.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.117596 restraints weight = 52815.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.118169 restraints weight = 32054.012| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25721 Z= 0.116 Angle : 0.549 8.761 34755 Z= 0.289 Chirality : 0.042 0.198 3830 Planarity : 0.004 0.044 4395 Dihedral : 4.568 39.454 3519 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.76 % Favored : 96.11 % Rotamer: Outliers : 1.92 % Allowed : 16.69 % Favored : 81.40 % 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: 0.55 (0.15), residues: 3164 helix: 1.74 (0.14), residues: 1436 sheet: -0.63 (0.26), residues: 385 loop : -0.83 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 374 HIS 0.011 0.001 HIS D 412 PHE 0.029 0.001 PHE B 56 TYR 0.017 0.001 TYR C 26 ARG 0.006 0.000 ARG C 30 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 1198) hydrogen bonds : angle 4.15840 ( 3447) SS BOND : bond 0.00524 ( 8) SS BOND : angle 1.56655 ( 16) covalent geometry : bond 0.00263 (25711) covalent geometry : angle 0.54803 (34739) Misc. bond : bond 0.00134 ( 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 311 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8347 (m-30) cc_final: 0.8099 (p0) REVERT: A 184 LEU cc_start: 0.8826 (mm) cc_final: 0.8448 (mm) REVERT: A 767 TRP cc_start: 0.7287 (m-90) cc_final: 0.6791 (m-90) REVERT: B 292 MET cc_start: 0.6994 (mmm) cc_final: 0.5551 (ptm) REVERT: B 361 MET cc_start: 0.5642 (mtm) cc_final: 0.5349 (mtp) REVERT: B 408 MET cc_start: 0.6075 (tmm) cc_final: 0.5577 (tmm) REVERT: B 483 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7975 (mt) REVERT: B 485 ARG cc_start: 0.5288 (mtp85) cc_final: 0.5012 (ptp-110) REVERT: C 97 ILE cc_start: 0.7911 (mt) cc_final: 0.7680 (pt) REVERT: C 116 ASP cc_start: 0.7706 (t0) cc_final: 0.7439 (p0) REVERT: C 269 GLU cc_start: 0.6413 (pm20) cc_final: 0.5938 (tp30) REVERT: C 407 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7275 (mpp) REVERT: C 479 LEU cc_start: 0.8183 (mt) cc_final: 0.7960 (mt) REVERT: C 585 MET cc_start: 0.8946 (mmt) cc_final: 0.8610 (mmt) REVERT: C 784 THR cc_start: 0.8131 (p) cc_final: 0.7724 (t) REVERT: D 18 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.5420 (m-10) REVERT: D 137 TYR cc_start: 0.7429 (p90) cc_final: 0.6889 (p90) REVERT: D 292 MET cc_start: 0.7306 (mmm) cc_final: 0.5808 (ptm) REVERT: D 304 ILE cc_start: 0.3991 (mm) cc_final: 0.3742 (mt) outliers start: 52 outliers final: 30 residues processed: 295 average time/residue: 0.3273 time to fit residues: 156.5403 Evaluate side-chains 257 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR 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 772 GLU 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 167 ASN Chi-restraints excluded: chain B residue 180 LEU 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 546 PHE 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 712 ILE Chi-restraints excluded: chain D residue 18 PHE 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: 9.9990 chunk 125 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 300 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 198 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 227 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.168259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.126488 restraints weight = 52487.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.119047 restraints weight = 53666.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.119659 restraints weight = 40299.548| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25721 Z= 0.121 Angle : 0.539 11.793 34755 Z= 0.282 Chirality : 0.042 0.150 3830 Planarity : 0.004 0.045 4395 Dihedral : 4.357 38.000 3519 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.36 % Favored : 95.51 % Rotamer: Outliers : 2.39 % Allowed : 17.05 % Favored : 80.55 % 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: 0.67 (0.15), residues: 3164 helix: 1.86 (0.14), residues: 1436 sheet: -0.59 (0.26), residues: 389 loop : -0.78 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 374 HIS 0.012 0.001 HIS D 412 PHE 0.033 0.001 PHE B 56 TYR 0.024 0.001 TYR D 127 ARG 0.007 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 1198) hydrogen bonds : angle 4.06900 ( 3447) SS BOND : bond 0.00572 ( 8) SS BOND : angle 1.21870 ( 16) covalent geometry : bond 0.00280 (25711) covalent geometry : angle 0.53890 (34739) Misc. bond : bond 0.00156 ( 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 320 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 255 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASP cc_start: 0.8325 (m-30) cc_final: 0.8083 (p0) REVERT: A 767 TRP cc_start: 0.7340 (m-90) cc_final: 0.6946 (m-90) REVERT: B 292 MET cc_start: 0.7020 (mmm) cc_final: 0.5566 (ptm) REVERT: B 361 MET cc_start: 0.5602 (mtm) cc_final: 0.5357 (mtp) REVERT: B 407 MET cc_start: 0.5528 (mtm) cc_final: 0.4775 (mmm) REVERT: B 480 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7313 (p) REVERT: B 483 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8000 (mt) REVERT: C 269 GLU cc_start: 0.6448 (pm20) cc_final: 0.6036 (tp30) REVERT: C 407 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7230 (mpp) REVERT: C 585 MET cc_start: 0.9046 (mmt) cc_final: 0.8696 (mmt) REVERT: C 673 TYR cc_start: 0.8725 (t80) cc_final: 0.8201 (t80) REVERT: C 784 THR cc_start: 0.8103 (p) cc_final: 0.7693 (t) REVERT: D 18 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.5356 (m-10) REVERT: D 137 TYR cc_start: 0.7357 (p90) cc_final: 0.6788 (p90) REVERT: D 292 MET cc_start: 0.7191 (mmm) cc_final: 0.5735 (ptm) REVERT: D 304 ILE cc_start: 0.4039 (mm) cc_final: 0.3779 (mt) REVERT: D 782 GLU cc_start: 0.6412 (mp0) cc_final: 0.6196 (tt0) outliers start: 65 outliers final: 46 residues processed: 301 average time/residue: 0.3307 time to fit residues: 161.4970 Evaluate side-chains 280 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 230 time to evaluate : 2.614 ------------------------------------------------------------------------------- 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 52 VAL 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 381 VAL Chi-restraints excluded: chain A residue 425 CYS 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 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 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 480 THR 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 B residue 704 LEU 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 376 GLU Chi-restraints excluded: chain C residue 407 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 D residue 18 PHE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 407 MET 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: 5.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 219 optimal weight: 0.0010 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- 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 = 0.4354 r_free = 0.4354 target = 0.165490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.123923 restraints weight = 52703.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.114234 restraints weight = 54252.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.114798 restraints weight = 33527.927| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25721 Z= 0.203 Angle : 0.597 12.461 34755 Z= 0.312 Chirality : 0.044 0.180 3830 Planarity : 0.004 0.049 4395 Dihedral : 4.675 38.062 3519 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 2.87 % Allowed : 17.16 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (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: 0.43 (0.15), residues: 3164 helix: 1.63 (0.14), residues: 1442 sheet: -0.76 (0.26), residues: 387 loop : -0.86 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 374 HIS 0.011 0.001 HIS D 412 PHE 0.031 0.002 PHE B 56 TYR 0.017 0.001 TYR B 77 ARG 0.006 0.001 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 1198) hydrogen bonds : angle 4.21955 ( 3447) SS BOND : bond 0.00388 ( 8) SS BOND : angle 1.32403 ( 16) covalent geometry : bond 0.00486 (25711) covalent geometry : angle 0.59599 (34739) Misc. bond : bond 0.00313 ( 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 317 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 239 time to evaluate : 2.894 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 247 ILE cc_start: 0.8299 (tp) cc_final: 0.8047 (tt) REVERT: B 361 MET cc_start: 0.5747 (mtm) cc_final: 0.5490 (mtp) REVERT: C 269 GLU cc_start: 0.6449 (pm20) cc_final: 0.5984 (tp30) REVERT: C 407 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7278 (mpp) REVERT: C 585 MET cc_start: 0.8929 (mmt) cc_final: 0.8681 (mmt) REVERT: C 784 THR cc_start: 0.8156 (p) cc_final: 0.7709 (t) REVERT: D 18 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5733 (m-10) REVERT: D 137 TYR cc_start: 0.7560 (p90) cc_final: 0.7287 (p90) REVERT: D 268 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7835 (tptm) REVERT: D 304 ILE cc_start: 0.4071 (mm) cc_final: 0.3805 (mt) REVERT: D 546 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8260 (p90) REVERT: D 782 GLU cc_start: 0.6507 (mp0) cc_final: 0.6210 (tt0) outliers start: 78 outliers final: 61 residues processed: 294 average time/residue: 0.3353 time to fit residues: 160.0055 Evaluate side-chains 282 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 2.577 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain A residue 246 GLN 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 688 GLU 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 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 46 HIS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 265 LEU 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 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 729 SER 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 31 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 546 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 157 optimal weight: 0.6980 chunk 239 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 290 optimal weight: 0.6980 chunk 258 optimal weight: 0.9990 chunk 299 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.167530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.125118 restraints weight = 52752.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.117161 restraints weight = 55598.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117071 restraints weight = 34660.574| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.5779 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= 0.118 Angle : 0.542 11.551 34755 Z= 0.281 Chirality : 0.042 0.242 3830 Planarity : 0.004 0.045 4395 Dihedral : 4.345 35.908 3519 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.46 % Favored : 95.42 % Rotamer: Outliers : 2.28 % Allowed : 17.72 % 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: 0.62 (0.15), residues: 3164 helix: 1.81 (0.14), residues: 1444 sheet: -0.62 (0.27), residues: 372 loop : -0.81 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 374 HIS 0.013 0.001 HIS D 412 PHE 0.028 0.001 PHE B 56 TYR 0.022 0.001 TYR C 26 ARG 0.007 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 1198) hydrogen bonds : angle 4.01842 ( 3447) SS BOND : bond 0.00142 ( 8) SS BOND : angle 0.99656 ( 16) covalent geometry : bond 0.00272 (25711) covalent geometry : angle 0.54148 (34739) Misc. bond : bond 0.00150 ( 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 310 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 248 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ILE cc_start: 0.8395 (tp) cc_final: 0.8148 (tt) REVERT: A 362 GLU cc_start: 0.7065 (pm20) cc_final: 0.6737 (pm20) REVERT: A 373 TYR cc_start: 0.8021 (m-80) cc_final: 0.7785 (m-80) REVERT: A 767 TRP cc_start: 0.7467 (m-90) cc_final: 0.7084 (m-90) REVERT: B 292 MET cc_start: 0.6857 (mmm) cc_final: 0.5478 (ptm) REVERT: B 361 MET cc_start: 0.5629 (mtm) cc_final: 0.5213 (mtp) REVERT: B 374 TRP cc_start: 0.6278 (t60) cc_final: 0.6017 (t60) REVERT: C 269 GLU cc_start: 0.6320 (pm20) cc_final: 0.5953 (tp30) REVERT: C 407 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7347 (mpp) REVERT: C 674 MET cc_start: 0.8118 (mtm) cc_final: 0.7858 (mtm) REVERT: C 784 THR cc_start: 0.8111 (p) cc_final: 0.7631 (t) REVERT: D 18 PHE cc_start: 0.6256 (OUTLIER) cc_final: 0.5267 (m-10) REVERT: D 137 TYR cc_start: 0.7455 (p90) cc_final: 0.6828 (p90) REVERT: D 292 MET cc_start: 0.7011 (mmm) cc_final: 0.5581 (ptm) REVERT: D 304 ILE cc_start: 0.3973 (mm) cc_final: 0.3690 (mt) REVERT: D 700 TYR cc_start: 0.7398 (t80) cc_final: 0.7138 (t80) REVERT: D 782 GLU cc_start: 0.6388 (mp0) cc_final: 0.6177 (tt0) outliers start: 62 outliers final: 53 residues processed: 292 average time/residue: 0.3453 time to fit residues: 162.3766 Evaluate side-chains 281 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 2.784 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 688 GLU 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 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 82 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 265 LEU 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 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 31 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 489 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 172 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 215 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 214 optimal weight: 0.0970 chunk 97 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.166773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.125849 restraints weight = 52839.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.116664 restraints weight = 55061.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.117354 restraints weight = 35312.009| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25721 Z= 0.144 Angle : 0.568 11.126 34755 Z= 0.293 Chirality : 0.043 0.222 3830 Planarity : 0.004 0.046 4395 Dihedral : 4.333 34.589 3519 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.93 % Favored : 94.94 % Rotamer: Outliers : 2.54 % Allowed : 17.83 % Favored : 79.63 % 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: 0.60 (0.15), residues: 3164 helix: 1.78 (0.14), residues: 1447 sheet: -0.61 (0.27), residues: 382 loop : -0.82 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 374 HIS 0.013 0.001 HIS D 412 PHE 0.024 0.001 PHE B 56 TYR 0.017 0.001 TYR C 26 ARG 0.006 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 1198) hydrogen bonds : angle 4.04556 ( 3447) SS BOND : bond 0.00142 ( 8) SS BOND : angle 1.01895 ( 16) covalent geometry : bond 0.00341 (25711) covalent geometry : angle 0.56797 (34739) Misc. bond : bond 0.00202 ( 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 314 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 245 time to evaluate : 2.589 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: A 362 GLU cc_start: 0.7042 (pm20) cc_final: 0.6820 (pm20) REVERT: A 373 TYR cc_start: 0.7878 (m-80) cc_final: 0.7609 (m-80) REVERT: B 292 MET cc_start: 0.6903 (mmm) cc_final: 0.5453 (ptm) REVERT: B 361 MET cc_start: 0.5717 (mtm) cc_final: 0.5348 (mtp) REVERT: B 661 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7683 (ptp90) REVERT: C 97 ILE cc_start: 0.7512 (mm) cc_final: 0.7116 (pt) REVERT: C 269 GLU cc_start: 0.6393 (pm20) cc_final: 0.6010 (tp30) REVERT: C 407 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7164 (mpp) REVERT: C 585 MET cc_start: 0.8985 (mmt) cc_final: 0.8649 (mmt) REVERT: C 784 THR cc_start: 0.8086 (p) cc_final: 0.7652 (t) REVERT: D 18 PHE cc_start: 0.6135 (OUTLIER) cc_final: 0.5264 (m-10) REVERT: D 137 TYR cc_start: 0.7432 (p90) cc_final: 0.6766 (p90) REVERT: D 304 ILE cc_start: 0.4052 (mm) cc_final: 0.3742 (mt) REVERT: D 782 GLU cc_start: 0.6299 (mp0) cc_final: 0.6097 (tt0) outliers start: 69 outliers final: 60 residues processed: 292 average time/residue: 0.3323 time to fit residues: 157.3929 Evaluate side-chains 297 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 234 time to evaluate : 2.899 ------------------------------------------------------------------------------- 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 48 ASP 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 180 LEU Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 493 LYS 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 688 GLU 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 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 661 ARG Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 265 LEU 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 493 LYS Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 488 VAL 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: 4.9990 chunk 197 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 287 optimal weight: 0.0040 chunk 150 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 = 0.4373 r_free = 0.4373 target = 0.167088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.125458 restraints weight = 52872.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.118098 restraints weight = 59886.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.116070 restraints weight = 41562.529| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.6049 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= 0.135 Angle : 0.562 10.760 34755 Z= 0.291 Chirality : 0.042 0.186 3830 Planarity : 0.004 0.046 4395 Dihedral : 4.294 32.767 3519 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.52 % Favored : 95.35 % Rotamer: Outliers : 2.58 % Allowed : 17.94 % Favored : 79.48 % 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: 0.64 (0.15), residues: 3164 helix: 1.85 (0.14), residues: 1441 sheet: -0.54 (0.27), residues: 368 loop : -0.85 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 262 HIS 0.013 0.001 HIS D 412 PHE 0.023 0.001 PHE A 658 TYR 0.017 0.001 TYR C 26 ARG 0.005 0.000 ARG C 30 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 1198) hydrogen bonds : angle 4.04698 ( 3447) SS BOND : bond 0.00255 ( 8) SS BOND : angle 1.16563 ( 16) covalent geometry : bond 0.00319 (25711) covalent geometry : angle 0.56146 (34739) Misc. bond : bond 0.00182 ( 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 324 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 254 time to evaluate : 2.736 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: A 97 ILE cc_start: 0.7268 (mm) cc_final: 0.6837 (pt) REVERT: A 373 TYR cc_start: 0.7981 (m-80) cc_final: 0.7666 (m-80) REVERT: A 453 ARG cc_start: 0.8244 (tpp80) cc_final: 0.8019 (tpt90) REVERT: B 93 HIS cc_start: 0.6015 (m-70) cc_final: 0.5786 (m-70) REVERT: B 292 MET cc_start: 0.7264 (mmm) cc_final: 0.5722 (ptm) REVERT: B 361 MET cc_start: 0.5807 (mtm) cc_final: 0.5420 (mtp) REVERT: B 634 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6963 (tp30) REVERT: B 661 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7707 (ptp90) REVERT: C 97 ILE cc_start: 0.7605 (mm) cc_final: 0.7277 (pt) REVERT: C 269 GLU cc_start: 0.6352 (pm20) cc_final: 0.5938 (tp30) REVERT: C 316 LEU cc_start: 0.3341 (mt) cc_final: 0.2831 (pp) REVERT: C 407 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7118 (mpp) REVERT: C 585 MET cc_start: 0.9001 (mmt) cc_final: 0.8661 (mmt) REVERT: C 784 THR cc_start: 0.8097 (p) cc_final: 0.7616 (t) REVERT: D 18 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.5290 (m-10) REVERT: D 74 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.6137 (t80) REVERT: D 137 TYR cc_start: 0.7429 (p90) cc_final: 0.6727 (p90) REVERT: D 304 ILE cc_start: 0.3973 (mm) cc_final: 0.3654 (mt) REVERT: D 700 TYR cc_start: 0.7381 (t80) cc_final: 0.7112 (t80) REVERT: D 782 GLU cc_start: 0.6371 (mp0) cc_final: 0.6152 (tt0) outliers start: 70 outliers final: 59 residues processed: 304 average time/residue: 0.3480 time to fit residues: 169.5982 Evaluate side-chains 300 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 237 time to evaluate : 2.932 ------------------------------------------------------------------------------- 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 82 VAL Chi-restraints excluded: chain A residue 89 CYS 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 381 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 425 CYS Chi-restraints excluded: chain A residue 493 LYS 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 688 GLU Chi-restraints excluded: chain A residue 773 CYS 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 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 661 ARG Chi-restraints excluded: chain B residue 704 LEU 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 376 GLU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 493 LYS Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 729 SER 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 31 VAL 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 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 488 VAL 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: 0.9990 chunk 220 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 311 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.167486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.125451 restraints weight = 52971.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.118004 restraints weight = 61346.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.116343 restraints weight = 37087.193| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25721 Z= 0.126 Angle : 0.572 10.660 34755 Z= 0.295 Chirality : 0.042 0.175 3830 Planarity : 0.004 0.046 4395 Dihedral : 4.239 32.089 3519 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 2.39 % Allowed : 18.53 % Favored : 79.08 % 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: 0.68 (0.15), residues: 3164 helix: 1.86 (0.14), residues: 1441 sheet: -0.51 (0.27), residues: 370 loop : -0.81 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 374 HIS 0.013 0.001 HIS D 412 PHE 0.051 0.001 PHE B 56 TYR 0.016 0.001 TYR C 26 ARG 0.008 0.000 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 1198) hydrogen bonds : angle 4.03272 ( 3447) SS BOND : bond 0.00181 ( 8) SS BOND : angle 2.38563 ( 16) covalent geometry : bond 0.00295 (25711) covalent geometry : angle 0.56971 (34739) Misc. bond : bond 0.00154 ( 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: 8699.33 seconds wall clock time: 151 minutes 59.06 seconds (9119.06 seconds total)