Starting phenix.real_space_refine on Sun Jul 5 11:10:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uea_26469/07_2026/7uea_26469.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uea_26469/07_2026/7uea_26469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uea_26469/07_2026/7uea_26469.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uea_26469/07_2026/7uea_26469.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uea_26469/07_2026/7uea_26469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uea_26469/07_2026/7uea_26469.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uea_26469/07_2026/7uea_26469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uea_26469/07_2026/7uea_26469.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.090 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 12 7.16 5 P 6 5.49 5 Mg 54 5.21 5 S 110 5.16 5 C 17882 2.51 5 N 3899 2.21 5 O 4348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26313 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5167 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 26, 'TRANS': 618} Chain breaks: 1 Chain: "a" Number of atoms: 5079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5079 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 25, 'TRANS': 607} Chain breaks: 2 Chain: "B" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 855 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain breaks: 1 Chain: "C" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 916 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "c" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 839 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "U" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2834 Classifications: {'peptide': 364} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 344} Chain: "V" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2805 Classifications: {'peptide': 360} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 340} Chain: "W" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2797 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain: "A" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 1269 Unusual residues: {' CA': 1, 'BCL': 12, 'F26': 1, 'F39': 1, 'G2O': 1, 'GS0': 1, 'LHG': 2, 'LMG': 5} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 1326 Unusual residues: {' CA': 1, 'BCL': 12, 'F26': 2, 'F39': 1, 'G2O': 3, 'GS0': 1, 'LHG': 3, 'LMG': 1, 'SF4': 1} Classifications: {'undetermined': 25} Link IDs: {None: 24} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'LHG': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "U" Number of atoms: 574 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 9, 574 Unusual residues: {'BCL': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "V" Number of atoms: 508 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 8, 508 Unusual residues: {'BCL': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "W" Number of atoms: 442 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 7, 442 Unusual residues: {'BCL': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3765 SG CYS A 536 58.524 52.760 71.955 1.00 73.17 S ATOM 3706 SG CYS A 527 63.367 53.464 75.665 1.00 69.88 S ATOM 8850 SG CYS a 536 64.136 56.528 70.010 1.00 63.48 S ATOM 8791 SG CYS a 527 62.933 50.380 69.822 1.00 82.75 S ATOM 10437 SG CYS B 143 67.907 49.677 80.521 1.00 41.30 S ATOM 10420 SG CYS B 140 70.042 43.458 80.528 1.00 42.07 S ATOM 10792 SG CYS B 191 68.146 46.066 86.049 1.00 45.14 S ATOM 10455 SG CYS B 146 73.190 48.465 83.545 1.00 58.20 S ATOM 10731 SG CYS B 182 83.878 52.649 88.039 1.00 49.75 S ATOM 10486 SG CYS B 150 81.271 51.896 82.638 1.00 67.48 S ATOM 10748 SG CYS B 185 77.459 50.338 86.534 1.00 37.67 S ATOM 10711 SG CYS B 179 82.861 46.809 87.065 1.00 39.68 S Time building chain proxies: 5.28, per 1000 atoms: 0.20 Number of scatterers: 26313 At special positions: 0 Unit cell: (108.16, 124.8, 185.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 12 26.01 Ca 2 19.99 S 110 16.00 P 6 15.00 Mg 54 11.99 O 4348 8.00 N 3899 7.00 C 17882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=22, symmetry=0 Number of additional bonds: simple=22, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 842.0 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 143 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 146 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 140 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 191 " pdb=" SF4 B 302 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 185 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 182 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 179 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 150 " pdb=" SF4 a 803 " pdb="FE1 SF4 a 803 " - pdb=" SG CYS A 536 " pdb="FE4 SF4 a 803 " - pdb=" SG CYS a 527 " pdb="FE2 SF4 a 803 " - pdb=" SG CYS A 527 " pdb="FE3 SF4 a 803 " - pdb=" SG CYS a 536 " Number of angles added : 36 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5078 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 12 sheets defined 48.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 71 through 97 Processing helix chain 'A' and resid 111 through 124 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 132 through 167 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 201 through 227 removed outlier: 4.799A pdb=" N GLY A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 241 through 263 Processing helix chain 'A' and resid 267 through 273 removed outlier: 4.405A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 273' Processing helix chain 'A' and resid 273 through 302 removed outlier: 4.466A pdb=" N PHE A 279 " --> pdb=" O MET A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.574A pdb=" N LYS A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 401 Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.806A pdb=" N ASN A 405 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE A 407 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 417 removed outlier: 5.330A pdb=" N GLY A 415 " --> pdb=" O TRP A 411 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 452 Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 468 through 475 removed outlier: 4.360A pdb=" N TRP A 473 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET A 474 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 506 removed outlier: 3.908A pdb=" N ALA A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 530 through 534 Processing helix chain 'A' and resid 539 through 564 removed outlier: 4.067A pdb=" N LYS A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY A 554 " --> pdb=" O TRP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 3.527A pdb=" N LYS A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 595 through 610 removed outlier: 4.379A pdb=" N PHE A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TRP A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 605 " --> pdb=" O TRP A 601 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR A 606 " --> pdb=" O THR A 602 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 632 removed outlier: 4.225A pdb=" N ALA A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 651 Processing helix chain 'A' and resid 669 through 696 removed outlier: 3.646A pdb=" N LEU A 675 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 691 " --> pdb=" O MET A 687 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY A 696 " --> pdb=" O PHE A 692 " (cutoff:3.500A) Processing helix chain 'a' and resid 60 through 64 removed outlier: 3.562A pdb=" N ILE a 64 " --> pdb=" O TRP a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 70 Processing helix chain 'a' and resid 71 through 96 Processing helix chain 'a' and resid 111 through 125 Proline residue: a 119 - end of helix Processing helix chain 'a' and resid 132 through 166 Processing helix chain 'a' and resid 186 through 191 Processing helix chain 'a' and resid 192 through 197 removed outlier: 4.378A pdb=" N ASN a 195 " --> pdb=" O VAL a 192 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY a 196 " --> pdb=" O VAL a 193 " (cutoff:3.500A) Processing helix chain 'a' and resid 201 through 227 removed outlier: 4.605A pdb=" N GLY a 207 " --> pdb=" O LYS a 203 " (cutoff:3.500A) Proline residue: a 208 - end of helix Processing helix chain 'a' and resid 238 through 263 removed outlier: 3.810A pdb=" N GLU a 242 " --> pdb=" O THR a 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 271 Processing helix chain 'a' and resid 274 through 302 Processing helix chain 'a' and resid 303 through 305 No H-bonds generated for 'chain 'a' and resid 303 through 305' Processing helix chain 'a' and resid 306 through 311 Processing helix chain 'a' and resid 311 through 316 removed outlier: 3.648A pdb=" N LYS a 315 " --> pdb=" O LYS a 311 " (cutoff:3.500A) Processing helix chain 'a' and resid 358 through 363 removed outlier: 3.504A pdb=" N PHE a 362 " --> pdb=" O SER a 358 " (cutoff:3.500A) Processing helix chain 'a' and resid 363 through 401 Processing helix chain 'a' and resid 403 through 407 removed outlier: 3.796A pdb=" N ILE a 407 " --> pdb=" O TYR a 404 " (cutoff:3.500A) Processing helix chain 'a' and resid 409 through 417 removed outlier: 5.235A pdb=" N GLY a 415 " --> pdb=" O TRP a 411 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP a 417 " --> pdb=" O THR a 413 " (cutoff:3.500A) Processing helix chain 'a' and resid 419 through 452 Processing helix chain 'a' and resid 453 through 456 Processing helix chain 'a' and resid 457 through 461 Processing helix chain 'a' and resid 471 through 475 Processing helix chain 'a' and resid 479 through 506 removed outlier: 3.844A pdb=" N ALA a 499 " --> pdb=" O PHE a 495 " (cutoff:3.500A) Processing helix chain 'a' and resid 510 through 516 Processing helix chain 'a' and resid 539 through 563 removed outlier: 4.186A pdb=" N LYS a 553 " --> pdb=" O LEU a 549 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY a 554 " --> pdb=" O TRP a 550 " (cutoff:3.500A) Processing helix chain 'a' and resid 580 through 587 removed outlier: 4.201A pdb=" N SER a 584 " --> pdb=" O LYS a 580 " (cutoff:3.500A) Processing helix chain 'a' and resid 595 through 608 removed outlier: 4.270A pdb=" N PHE a 600 " --> pdb=" O ILE a 596 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TRP a 601 " --> pdb=" O PHE a 597 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR a 606 " --> pdb=" O THR a 602 " (cutoff:3.500A) Processing helix chain 'a' and resid 610 through 632 removed outlier: 3.763A pdb=" N PHE a 628 " --> pdb=" O TRP a 624 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA a 629 " --> pdb=" O PHE a 625 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL a 630 " --> pdb=" O ILE a 626 " (cutoff:3.500A) Processing helix chain 'a' and resid 634 through 657 Processing helix chain 'a' and resid 669 through 695 removed outlier: 3.774A pdb=" N LEU a 691 " --> pdb=" O MET a 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'C' and resid 10 through 32 removed outlier: 4.043A pdb=" N GLY C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 72 removed outlier: 3.767A pdb=" N SER C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.886A pdb=" N SER C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Proline residue: C 82 - end of helix removed outlier: 3.813A pdb=" N ARG C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 125 Processing helix chain 'c' and resid 23 through 31 Processing helix chain 'c' and resid 42 through 73 removed outlier: 3.839A pdb=" N LEU c 46 " --> pdb=" O ILE c 42 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER c 71 " --> pdb=" O GLY c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 79 removed outlier: 3.968A pdb=" N LEU c 79 " --> pdb=" O LYS c 76 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 99 Processing helix chain 'c' and resid 115 through 125 Processing helix chain 'D' and resid 63 through 72 Processing helix chain 'U' and resid 127 through 134 Processing helix chain 'U' and resid 156 through 173 removed outlier: 3.665A pdb=" N GLY U 171 " --> pdb=" O VAL U 167 " (cutoff:3.500A) Processing helix chain 'U' and resid 175 through 185 removed outlier: 4.554A pdb=" N ARG U 181 " --> pdb=" O ASN U 177 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP U 182 " --> pdb=" O ASP U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 188 through 196 removed outlier: 3.743A pdb=" N ASN U 194 " --> pdb=" O PHE U 190 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 238 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 291 through 303 removed outlier: 3.956A pdb=" N LEU U 295 " --> pdb=" O PRO U 291 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET U 300 " --> pdb=" O VAL U 296 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL U 301 " --> pdb=" O HIS U 297 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS U 303 " --> pdb=" O GLY U 299 " (cutoff:3.500A) Processing helix chain 'U' and resid 343 through 354 removed outlier: 3.568A pdb=" N LYS U 354 " --> pdb=" O GLU U 350 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 134 removed outlier: 3.877A pdb=" N ARG V 131 " --> pdb=" O SER V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 173 Processing helix chain 'V' and resid 175 through 185 removed outlier: 4.637A pdb=" N ARG V 181 " --> pdb=" O ASN V 177 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP V 182 " --> pdb=" O ASP V 178 " (cutoff:3.500A) Processing helix chain 'V' and resid 187 through 196 removed outlier: 4.133A pdb=" N THR V 191 " --> pdb=" O GLY V 187 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN V 194 " --> pdb=" O PHE V 190 " (cutoff:3.500A) Processing helix chain 'V' and resid 233 through 238 Processing helix chain 'V' and resid 238 through 243 removed outlier: 3.694A pdb=" N PHE V 243 " --> pdb=" O TRP V 239 " (cutoff:3.500A) Processing helix chain 'V' and resid 291 through 303 removed outlier: 3.771A pdb=" N LEU V 295 " --> pdb=" O PRO V 291 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL V 301 " --> pdb=" O HIS V 297 " (cutoff:3.500A) Processing helix chain 'V' and resid 343 through 354 Processing helix chain 'W' and resid 127 through 133 removed outlier: 3.580A pdb=" N ASN W 133 " --> pdb=" O ALA W 129 " (cutoff:3.500A) Processing helix chain 'W' and resid 156 through 172 Processing helix chain 'W' and resid 175 through 185 removed outlier: 4.119A pdb=" N ARG W 181 " --> pdb=" O ASN W 177 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP W 182 " --> pdb=" O ASP W 178 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE W 185 " --> pdb=" O ARG W 181 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 197 removed outlier: 4.023A pdb=" N ASN W 194 " --> pdb=" O PHE W 190 " (cutoff:3.500A) Processing helix chain 'W' and resid 233 through 238 removed outlier: 3.854A pdb=" N SER W 237 " --> pdb=" O VAL W 233 " (cutoff:3.500A) Processing helix chain 'W' and resid 291 through 303 removed outlier: 4.061A pdb=" N LEU W 295 " --> pdb=" O PRO W 291 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL W 301 " --> pdb=" O HIS W 297 " (cutoff:3.500A) Processing helix chain 'W' and resid 341 through 354 removed outlier: 4.449A pdb=" N TYR W 345 " --> pdb=" O SER W 341 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS W 354 " --> pdb=" O GLU W 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 101 removed outlier: 3.575A pdb=" N ALA A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AA3, first strand: chain 'B' and resid 157 through 160 Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 53 removed outlier: 5.702A pdb=" N GLU D 32 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR D 78 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR D 34 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL D 110 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE D 79 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'U' and resid 198 through 200 Processing sheet with id=AA6, first strand: chain 'U' and resid 204 through 205 removed outlier: 3.749A pdb=" N GLY U 142 " --> pdb=" O GLY U 229 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N THR U 112 " --> pdb=" O PRO U 153 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP U 270 " --> pdb=" O GLU U 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'U' and resid 277 through 279 Processing sheet with id=AA8, first strand: chain 'V' and resid 198 through 200 removed outlier: 6.878A pdb=" N ARG V 224 " --> pdb=" O VAL V 205 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL V 205 " --> pdb=" O ARG V 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'V' and resid 198 through 200 removed outlier: 3.837A pdb=" N GLY V 231 " --> pdb=" O MET V 140 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET V 140 " --> pdb=" O GLY V 231 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N THR V 112 " --> pdb=" O PRO V 153 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE V 64 " --> pdb=" O LEU V 58 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA V 12 " --> pdb=" O ASP V 310 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLN V 312 " --> pdb=" O ALA V 12 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER V 14 " --> pdb=" O GLN V 312 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LYS V 314 " --> pdb=" O SER V 14 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR V 16 " --> pdb=" O LYS V 314 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL V 316 " --> pdb=" O TYR V 16 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE V 18 " --> pdb=" O VAL V 316 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'V' and resid 277 through 279 removed outlier: 6.739A pdb=" N LEU V 363 " --> pdb=" O ARG V 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'W' and resid 204 through 211 removed outlier: 5.353A pdb=" N VAL W 205 " --> pdb=" O ARG W 224 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG W 224 " --> pdb=" O VAL W 205 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR W 112 " --> pdb=" O PRO W 153 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N PHE W 64 " --> pdb=" O LEU W 58 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU W 58 " --> pdb=" O PHE W 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 277 through 281 removed outlier: 3.553A pdb=" N ALA W 280 " --> pdb=" O LEU W 284 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU W 284 " --> pdb=" O ALA W 280 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ILE W 362 " --> pdb=" O ILE W 287 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU W 363 " --> pdb=" O ARG W 324 " (cutoff:3.500A) 1310 hydrogen bonds defined for protein. 3747 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: 5.08 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.36: 7642 1.36 - 1.63: 19344 1.63 - 1.89: 170 1.89 - 2.15: 161 2.15 - 2.41: 91 Bond restraints: 27408 Sorted by residual: bond pdb=" ND G2O A 824 " pdb="MG G2O A 824 " ideal model delta sigma weight residual 2.005 2.415 -0.410 2.00e-02 2.50e+03 4.20e+02 bond pdb=" ND G2O a 805 " pdb="MG G2O a 805 " ideal model delta sigma weight residual 2.005 2.362 -0.357 2.00e-02 2.50e+03 3.18e+02 bond pdb=" ND G2O a 802 " pdb="MG G2O a 802 " ideal model delta sigma weight residual 2.005 2.344 -0.339 2.00e-02 2.50e+03 2.87e+02 bond pdb=" ND G2O a 801 " pdb="MG G2O a 801 " ideal model delta sigma weight residual 2.005 2.307 -0.302 2.00e-02 2.50e+03 2.27e+02 bond pdb=" NC G2O a 801 " pdb="MG G2O a 801 " ideal model delta sigma weight residual 2.065 2.344 -0.279 2.00e-02 2.50e+03 1.94e+02 ... (remaining 27403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 37291 4.41 - 8.83: 465 8.83 - 13.24: 78 13.24 - 17.66: 21 17.66 - 22.07: 96 Bond angle restraints: 37951 Sorted by residual: angle pdb=" NB BCL U 405 " pdb="MG BCL U 405 " pdb=" ND BCL U 405 " ideal model delta sigma weight residual 157.70 179.77 -22.07 2.51e+00 1.58e-01 7.71e+01 angle pdb=" NB BCL A 806 " pdb="MG BCL A 806 " pdb=" ND BCL A 806 " ideal model delta sigma weight residual 157.70 179.69 -21.99 2.51e+00 1.58e-01 7.66e+01 angle pdb=" NB BCL U 402 " pdb="MG BCL U 402 " pdb=" ND BCL U 402 " ideal model delta sigma weight residual 157.70 179.68 -21.98 2.51e+00 1.58e-01 7.65e+01 angle pdb=" NB BBCL W 407 " pdb="MG BBCL W 407 " pdb=" ND BBCL W 407 " ideal model delta sigma weight residual 157.70 179.67 -21.97 2.51e+00 1.58e-01 7.64e+01 angle pdb=" NB BCL a 809 " pdb="MG BCL a 809 " pdb=" ND BCL a 809 " ideal model delta sigma weight residual 157.70 179.64 -21.94 2.51e+00 1.58e-01 7.62e+01 ... (remaining 37946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 14287 35.83 - 71.65: 491 71.65 - 107.48: 54 107.48 - 143.30: 14 143.30 - 179.13: 2 Dihedral angle restraints: 14848 sinusoidal: 6888 harmonic: 7960 Sorted by residual: dihedral pdb=" CA ALA W 327 " pdb=" C ALA W 327 " pdb=" N PRO W 328 " pdb=" CA PRO W 328 " ideal model delta harmonic sigma weight residual -180.00 -143.81 -36.19 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CA LYS D 40 " pdb=" C LYS D 40 " pdb=" N ARG D 41 " pdb=" CA ARG D 41 " ideal model delta harmonic sigma weight residual 180.00 148.65 31.35 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA ALA W 326 " pdb=" C ALA W 326 " pdb=" N ALA W 327 " pdb=" CA ALA W 327 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 14845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.146: 3775 1.146 - 2.293: 0 2.293 - 3.439: 14 3.439 - 4.585: 0 4.585 - 5.732: 3 Chirality restraints: 3792 Sorted by residual: chirality pdb=" C3C GS0 a 804 " pdb=" C2C GS0 a 804 " pdb=" C4C GS0 a 804 " pdb=" CAC GS0 a 804 " both_signs ideal model delta sigma weight residual False 2.77 -2.96 5.73 2.00e-01 2.50e+01 8.21e+02 chirality pdb=" C13 GS0 A 801 " pdb=" C12 GS0 A 801 " pdb=" C14 GS0 A 801 " pdb=" C15 GS0 A 801 " both_signs ideal model delta sigma weight residual False 2.54 -2.75 5.29 2.00e-01 2.50e+01 7.00e+02 chirality pdb=" C8 G2O a 801 " pdb=" C10 G2O a 801 " pdb=" C7 G2O a 801 " pdb=" C9 G2O a 801 " both_signs ideal model delta sigma weight residual False 2.51 -2.26 4.77 2.00e-01 2.50e+01 5.69e+02 ... (remaining 3789 not shown) Planarity restraints: 4594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 F26 A 815 " 0.331 2.00e-02 2.50e+03 4.05e-01 2.05e+03 pdb=" C19 F26 A 815 " -0.351 2.00e-02 2.50e+03 pdb=" C23 F26 A 815 " 0.142 2.00e-02 2.50e+03 pdb=" C24 F26 A 815 " -0.590 2.00e-02 2.50e+03 pdb=" C27 F26 A 815 " 0.467 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C G2O A 824 " -0.172 2.00e-02 2.50e+03 2.63e-01 1.73e+03 pdb=" C2C G2O A 824 " 0.036 2.00e-02 2.50e+03 pdb=" C3C G2O A 824 " 0.040 2.00e-02 2.50e+03 pdb=" C4C G2O A 824 " -0.154 2.00e-02 2.50e+03 pdb=" CAC G2O A 824 " 0.226 2.00e-02 2.50e+03 pdb=" CHC G2O A 824 " -0.266 2.00e-02 2.50e+03 pdb=" CHD G2O A 824 " -0.238 2.00e-02 2.50e+03 pdb=" CMC G2O A 824 " 0.201 2.00e-02 2.50e+03 pdb=" NC G2O A 824 " -0.264 2.00e-02 2.50e+03 pdb="MG G2O A 824 " 0.591 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 F26 a 820 " 0.123 2.00e-02 2.50e+03 3.36e-01 1.41e+03 pdb=" C17 F26 a 820 " -0.152 2.00e-02 2.50e+03 pdb=" C18 F26 a 820 " 0.586 2.00e-02 2.50e+03 pdb=" C22 F26 a 820 " -0.398 2.00e-02 2.50e+03 pdb=" C8 F26 a 820 " -0.158 2.00e-02 2.50e+03 ... (remaining 4591 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 37 2.35 - 2.99: 12388 2.99 - 3.62: 41048 3.62 - 4.26: 68126 4.26 - 4.90: 113815 Nonbonded interactions: 235414 Sorted by model distance: nonbonded pdb=" OE1 GLU a 603 " pdb=" OD1 ASN a 695 " model vdw 1.709 3.040 nonbonded pdb=" OE1 GLU A 603 " pdb=" OD1 ASN A 695 " model vdw 1.815 3.040 nonbonded pdb=" O PHE A 692 " pdb=" ND2 ASN A 695 " model vdw 1.955 3.120 nonbonded pdb=" O GLY A 529 " pdb=" OG1 THR A 535 " model vdw 2.016 3.040 nonbonded pdb=" O PHE A 108 " pdb=" NH2 ARG c 104 " model vdw 2.094 3.120 ... (remaining 235409 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 59 through 171 or resid 180 through 333 or resid 343 throu \ gh 708 or resid 805 through 809 or (resid 810 and (name NB or name ND or name C1 \ A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or nam \ e C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4B or \ name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or name CB \ A or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or nam \ e CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or \ name CMD or name NA or name NC or name O1A or name O1D or name O2A or name O2D \ or name OBB or name OBD or name MG )) or resid 811 through 813)) selection = (chain 'a' and (resid 59 through 708 or resid 806 through 813 or (resid 814 and \ (name NB or name ND or name C1 or name C10 or name C11 or name C12 or name C13 o \ r name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C \ 1A or name C1B or name C1C or name C1D or name C2 or name C2A or name C2B or nam \ e C2C or name C2D or name C3 or name C3A or name C3B or name C3C or name C3D or \ name C4 or name C4A or name C4B or name C4C or name C4D or name C5 or name C6 or \ name C7 or name C8 or name C9 or name CAA or name CAB or name CAC or name CAD o \ r name CBA or name CBB or name CBC or name CBD or name CED or name CGA or name C \ GD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or na \ me CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2A or \ name O2D or name OBB or name OBD or name MG )))) } ncs_group { reference = (chain 'C' and resid 21 through 125) selection = chain 'c' } ncs_group { reference = (chain 'U' and (resid 8 through 406 or (resid 407 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )))) selection = (chain 'V' and (resid 8 through 406 or (resid 407 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )))) selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.310 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.650 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 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 : 0.020 0.852 27442 Z= 1.459 Angle : 1.617 22.070 37987 Z= 0.618 Chirality : 0.230 5.732 3792 Planarity : 0.024 0.405 4594 Dihedral : 18.277 179.127 9770 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2767 helix: 0.57 (0.15), residues: 1133 sheet: -0.30 (0.22), residues: 520 loop : -1.22 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 47 TYR 0.018 0.001 TYR A 681 PHE 0.025 0.002 PHE a 625 TRP 0.011 0.001 TRP C 52 HIS 0.006 0.001 HIS U 111 Details of bonding type rmsd/Z covalent geometry : bond 0.01273 / 0.62 (27408) covalent geometry : angle 1.58939 / 0.62 (37951) hydrogen bonds : bond 0.11894 / 8.27 ( 1308) hydrogen bonds : angle 6.21931 / 4.52 ( 3747) metal coordination : bond 0.00247 / 0.15 ( 12) metal coordination : angle 9.81509 / 5.92 ( 36) Misc. bond : bond 0.54055 / 32.67 ( 22) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 778 time to evaluate : 0.828 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: A 90 MET cc_start: 0.8945 (mmm) cc_final: 0.8656 (mmp) REVERT: A 130 SER cc_start: 0.8700 (t) cc_final: 0.8459 (m) REVERT: A 168 ASN cc_start: 0.8535 (t0) cc_final: 0.8277 (t0) REVERT: A 176 ARG cc_start: 0.6966 (ptt90) cc_final: 0.6712 (ptt90) REVERT: A 179 ASN cc_start: 0.8830 (t0) cc_final: 0.8614 (t0) REVERT: A 204 GLU cc_start: 0.8182 (tp30) cc_final: 0.7777 (tp30) REVERT: A 241 SER cc_start: 0.8841 (p) cc_final: 0.8068 (m) REVERT: A 303 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7733 (mm110) REVERT: A 310 TYR cc_start: 0.8821 (m-80) cc_final: 0.8563 (m-80) REVERT: A 313 LEU cc_start: 0.8580 (tp) cc_final: 0.8308 (mt) REVERT: A 315 LYS cc_start: 0.8359 (tptp) cc_final: 0.8084 (mttm) REVERT: A 344 LYS cc_start: 0.6008 (ttpt) cc_final: 0.5757 (mttt) REVERT: A 521 ASN cc_start: 0.8441 (m-40) cc_final: 0.8006 (m-40) REVERT: A 584 SER cc_start: 0.8807 (t) cc_final: 0.8566 (p) REVERT: A 634 ASP cc_start: 0.8657 (p0) cc_final: 0.8413 (p0) REVERT: A 669 THR cc_start: 0.8750 (m) cc_final: 0.8549 (p) REVERT: a 137 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6504 (mm-30) REVERT: a 168 ASN cc_start: 0.8109 (t0) cc_final: 0.7707 (t0) REVERT: a 193 VAL cc_start: 0.8049 (m) cc_final: 0.7834 (m) REVERT: a 213 MET cc_start: 0.7036 (mtt) cc_final: 0.6767 (mtm) REVERT: a 218 LEU cc_start: 0.7418 (tt) cc_final: 0.7098 (mm) REVERT: a 245 MET cc_start: 0.6917 (tpp) cc_final: 0.6653 (tpp) REVERT: a 274 ASP cc_start: 0.7845 (p0) cc_final: 0.7588 (p0) REVERT: a 296 ILE cc_start: 0.8856 (mt) cc_final: 0.8528 (tt) REVERT: a 315 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7259 (tptm) REVERT: a 377 ILE cc_start: 0.8413 (mt) cc_final: 0.8168 (mt) REVERT: a 378 ILE cc_start: 0.8960 (tt) cc_final: 0.8711 (tt) REVERT: a 411 TRP cc_start: 0.7135 (m100) cc_final: 0.6855 (m-90) REVERT: a 424 ILE cc_start: 0.8408 (mt) cc_final: 0.8198 (mt) REVERT: a 468 LEU cc_start: 0.8185 (mt) cc_final: 0.7916 (mt) REVERT: a 592 TYR cc_start: 0.8033 (m-80) cc_final: 0.7635 (m-80) REVERT: a 630 VAL cc_start: 0.9172 (m) cc_final: 0.8938 (m) REVERT: a 645 GLN cc_start: 0.8646 (mt0) cc_final: 0.7959 (mt0) REVERT: a 646 THR cc_start: 0.8561 (m) cc_final: 0.8108 (p) REVERT: C 90 MET cc_start: 0.6904 (mtp) cc_final: 0.6651 (mtp) REVERT: D 49 ILE cc_start: 0.7352 (mt) cc_final: 0.7007 (tp) REVERT: D 78 TYR cc_start: 0.6074 (m-80) cc_final: 0.5585 (m-10) REVERT: U 31 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7740 (mtmm) REVERT: U 52 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7813 (tttt) REVERT: U 96 ARG cc_start: 0.8500 (ttm170) cc_final: 0.7990 (ttm170) REVERT: U 103 MET cc_start: 0.7731 (ttp) cc_final: 0.7363 (tmm) REVERT: U 140 MET cc_start: 0.7820 (tpt) cc_final: 0.7567 (mtt) REVERT: U 204 GLU cc_start: 0.7021 (tt0) cc_final: 0.6767 (mt-10) REVERT: U 232 MET cc_start: 0.8102 (mtp) cc_final: 0.7885 (mtm) REVERT: U 238 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7522 (mtm-85) REVERT: U 241 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7496 (mt-10) REVERT: U 314 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7748 (ttmt) REVERT: U 325 TYR cc_start: 0.7236 (t80) cc_final: 0.6760 (t80) REVERT: U 361 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6890 (mt-10) REVERT: V 31 LYS cc_start: 0.7863 (mttt) cc_final: 0.7293 (mttt) REVERT: V 35 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7876 (ttpp) REVERT: V 56 LYS cc_start: 0.7902 (tmmt) cc_final: 0.7612 (tptt) REVERT: V 59 ASP cc_start: 0.6192 (t0) cc_final: 0.5805 (p0) REVERT: V 268 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8400 (ttpt) REVERT: V 272 GLU cc_start: 0.7789 (tt0) cc_final: 0.7461 (tt0) REVERT: V 321 TYR cc_start: 0.7949 (m-10) cc_final: 0.7444 (m-10) REVERT: V 359 GLN cc_start: 0.7821 (tt0) cc_final: 0.7569 (tt0) REVERT: W 55 VAL cc_start: 0.8582 (t) cc_final: 0.8380 (t) REVERT: W 64 PHE cc_start: 0.7405 (m-80) cc_final: 0.6968 (m-80) REVERT: W 114 SER cc_start: 0.7539 (m) cc_final: 0.7330 (t) REVERT: W 122 LEU cc_start: 0.8062 (mt) cc_final: 0.7850 (mt) REVERT: W 127 SER cc_start: 0.8724 (t) cc_final: 0.8356 (p) REVERT: W 144 GLN cc_start: 0.6735 (mt0) cc_final: 0.6351 (mt0) REVERT: W 180 ILE cc_start: 0.8878 (tp) cc_final: 0.8620 (tp) REVERT: W 182 ASP cc_start: 0.7081 (m-30) cc_final: 0.6847 (m-30) REVERT: W 268 LYS cc_start: 0.7530 (ttmt) cc_final: 0.7093 (pttp) REVERT: W 278 VAL cc_start: 0.8583 (t) cc_final: 0.8114 (m) REVERT: W 292 LEU cc_start: 0.8452 (mp) cc_final: 0.8151 (mp) outliers start: 0 outliers final: 0 residues processed: 778 average time/residue: 0.1808 time to fit residues: 219.3127 Evaluate side-chains 632 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 632 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN A 167 HIS A 171 ASN A 375 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS a 74 GLN ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 262 ASN ** a 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 645 GLN a 699 GLN B 227 HIS U 111 HIS U 144 GLN U 146 HIS V 306 ASN W 13 HIS W 37 ASN W 136 ASN ** W 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 253 GLN W 306 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.190773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.173470 restraints weight = 36849.861| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.09 r_work: 0.3725 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 27442 Z= 0.170 Angle : 0.921 31.877 37987 Z= 0.350 Chirality : 0.045 0.283 3792 Planarity : 0.005 0.059 4594 Dihedral : 16.278 168.626 4795 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.02 % Rotamer: Outliers : 2.75 % Allowed : 15.06 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2767 helix: 0.77 (0.15), residues: 1152 sheet: -0.29 (0.22), residues: 517 loop : -1.15 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 199 TYR 0.023 0.002 TYR a 404 PHE 0.023 0.002 PHE a 697 TRP 0.011 0.001 TRP C 52 HIS 0.012 0.001 HIS W 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (27408) covalent geometry : angle 0.83802 / 0.35 (37951) hydrogen bonds : bond 0.04383 / 2.97 ( 1308) hydrogen bonds : angle 5.40194 / 3.93 ( 3747) metal coordination : bond 0.01099 / 0.62 ( 12) metal coordination : angle 12.44008 / 7.64 ( 36) Misc. bond : bond 0.04455 / 3.05 ( 22) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 641 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8369 (mtmm) cc_final: 0.8030 (mtmm) REVERT: A 90 MET cc_start: 0.9159 (mmm) cc_final: 0.8785 (mmt) REVERT: A 130 SER cc_start: 0.8608 (t) cc_final: 0.8373 (m) REVERT: A 132 LYS cc_start: 0.7680 (ttpp) cc_final: 0.7387 (ttpp) REVERT: A 168 ASN cc_start: 0.8536 (t0) cc_final: 0.8279 (t0) REVERT: A 238 THR cc_start: 0.6472 (p) cc_final: 0.6229 (p) REVERT: A 245 MET cc_start: 0.8589 (mmm) cc_final: 0.8204 (tpp) REVERT: A 275 MET cc_start: 0.6872 (mmp) cc_final: 0.6222 (mtm) REVERT: A 290 ASN cc_start: 0.9274 (t0) cc_final: 0.8784 (m-40) REVERT: A 301 PHE cc_start: 0.8264 (m-10) cc_final: 0.7967 (m-80) REVERT: A 303 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7480 (mm110) REVERT: A 310 TYR cc_start: 0.8800 (m-80) cc_final: 0.8555 (m-80) REVERT: A 315 LYS cc_start: 0.8462 (tptp) cc_final: 0.8030 (mttm) REVERT: A 316 LEU cc_start: 0.8195 (mt) cc_final: 0.7973 (mt) REVERT: A 319 TYR cc_start: 0.8382 (m-80) cc_final: 0.8161 (m-80) REVERT: A 485 MET cc_start: 0.7593 (tpt) cc_final: 0.7356 (tpt) REVERT: A 519 LYS cc_start: 0.7608 (pttt) cc_final: 0.7060 (ptmt) REVERT: A 521 ASN cc_start: 0.8891 (m-40) cc_final: 0.8506 (m-40) REVERT: A 548 MET cc_start: 0.7830 (mtm) cc_final: 0.7584 (mtm) REVERT: A 584 SER cc_start: 0.8972 (t) cc_final: 0.8729 (p) REVERT: a 60 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6593 (tttt) REVERT: a 82 LEU cc_start: 0.8420 (mt) cc_final: 0.8121 (mm) REVERT: a 114 TYR cc_start: 0.8316 (t80) cc_final: 0.8084 (t80) REVERT: a 137 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6589 (mm-30) REVERT: a 162 TRP cc_start: 0.7359 (t-100) cc_final: 0.7130 (t-100) REVERT: a 168 ASN cc_start: 0.7686 (t0) cc_final: 0.7275 (t0) REVERT: a 274 ASP cc_start: 0.7843 (p0) cc_final: 0.7290 (p0) REVERT: a 296 ILE cc_start: 0.8731 (mt) cc_final: 0.8439 (tt) REVERT: a 315 LYS cc_start: 0.7877 (mmtt) cc_final: 0.7261 (tptm) REVERT: a 323 GLU cc_start: 0.8012 (tp30) cc_final: 0.7620 (tm-30) REVERT: a 355 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7742 (mp) REVERT: a 378 ILE cc_start: 0.8964 (tt) cc_final: 0.8740 (tt) REVERT: a 401 ASN cc_start: 0.7710 (p0) cc_final: 0.6830 (m-40) REVERT: a 403 MET cc_start: 0.6759 (tpp) cc_final: 0.5017 (tmm) REVERT: a 411 TRP cc_start: 0.7253 (m100) cc_final: 0.6911 (m-90) REVERT: a 424 ILE cc_start: 0.8286 (mt) cc_final: 0.8040 (mt) REVERT: a 440 TYR cc_start: 0.8863 (t80) cc_final: 0.8602 (t80) REVERT: a 468 LEU cc_start: 0.8440 (mt) cc_final: 0.8190 (mt) REVERT: a 483 TRP cc_start: 0.7913 (t60) cc_final: 0.7492 (t60) REVERT: a 561 TYR cc_start: 0.8470 (t80) cc_final: 0.8236 (t80) REVERT: a 646 THR cc_start: 0.8541 (m) cc_final: 0.8141 (p) REVERT: a 700 THR cc_start: 0.7622 (p) cc_final: 0.7406 (t) REVERT: C 50 MET cc_start: 0.6554 (tmm) cc_final: 0.6185 (tmm) REVERT: C 90 MET cc_start: 0.7148 (mtp) cc_final: 0.6781 (mtp) REVERT: c 39 HIS cc_start: 0.4247 (m90) cc_final: 0.4015 (m170) REVERT: c 99 TYR cc_start: 0.6760 (t80) cc_final: 0.6168 (t80) REVERT: U 31 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7790 (mtmm) REVERT: U 85 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6985 (tt0) REVERT: U 88 ILE cc_start: 0.8494 (mt) cc_final: 0.8280 (pt) REVERT: U 103 MET cc_start: 0.8023 (ttp) cc_final: 0.7494 (tmm) REVERT: U 133 ASN cc_start: 0.7729 (m-40) cc_final: 0.7309 (t0) REVERT: U 204 GLU cc_start: 0.7481 (tt0) cc_final: 0.7268 (mt-10) REVERT: U 238 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7523 (mtm-85) REVERT: U 241 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7447 (mt-10) REVERT: U 314 LYS cc_start: 0.8392 (ttpt) cc_final: 0.8157 (ttpt) REVERT: U 325 TYR cc_start: 0.7649 (t80) cc_final: 0.7126 (t80) REVERT: U 361 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7183 (mt-10) REVERT: V 35 LYS cc_start: 0.7936 (ttmt) cc_final: 0.7657 (ttpp) REVERT: V 59 ASP cc_start: 0.6586 (t0) cc_final: 0.6123 (p0) REVERT: V 255 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7339 (mm-30) REVERT: V 268 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8458 (ttpt) REVERT: V 321 TYR cc_start: 0.8228 (m-10) cc_final: 0.7602 (m-10) REVERT: W 50 ASP cc_start: 0.6890 (t0) cc_final: 0.5753 (p0) REVERT: W 64 PHE cc_start: 0.7432 (m-80) cc_final: 0.6917 (m-80) REVERT: W 66 ARG cc_start: 0.6832 (ttp-170) cc_final: 0.6433 (ttm170) REVERT: W 72 GLU cc_start: 0.7241 (mp0) cc_final: 0.6201 (mp0) REVERT: W 151 LYS cc_start: 0.7369 (mmtm) cc_final: 0.7168 (mptt) REVERT: W 180 ILE cc_start: 0.8888 (tp) cc_final: 0.8642 (tp) REVERT: W 268 LYS cc_start: 0.7539 (ttmt) cc_final: 0.7102 (pttp) REVERT: W 292 LEU cc_start: 0.8639 (mp) cc_final: 0.8181 (mp) REVERT: W 314 LYS cc_start: 0.7691 (ttmt) cc_final: 0.7033 (ttpt) REVERT: W 325 TYR cc_start: 0.7527 (t80) cc_final: 0.6923 (t80) outliers start: 64 outliers final: 34 residues processed: 668 average time/residue: 0.1694 time to fit residues: 180.4614 Evaluate side-chains 637 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 601 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 225 TRP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain a residue 60 LYS Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 133 THR Chi-restraints excluded: chain a residue 355 LEU Chi-restraints excluded: chain a residue 413 THR Chi-restraints excluded: chain a residue 420 VAL Chi-restraints excluded: chain a residue 661 VAL Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 127 SER Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 202 ARG Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain U residue 317 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain W residue 18 ILE Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 136 ASN Chi-restraints excluded: chain W residue 147 ASP Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 332 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 121 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 390 HIS A 393 GLN a 150 HIS ** a 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 541 GLN a 699 GLN B 166 GLN C 38 ASN U 111 HIS V 156 ASN ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 111 HIS ** W 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 136 ASN ** W 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 227 HIS W 253 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.178115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.160554 restraints weight = 37228.759| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.05 r_work: 0.3628 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.383 27442 Z= 0.381 Angle : 1.028 32.563 37987 Z= 0.397 Chirality : 0.048 0.310 3792 Planarity : 0.006 0.074 4594 Dihedral : 15.323 176.873 4795 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.19 % Rotamer: Outliers : 4.63 % Allowed : 16.95 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 2767 helix: 0.63 (0.15), residues: 1156 sheet: -0.48 (0.21), residues: 517 loop : -1.32 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG V 250 TYR 0.038 0.003 TYR A 321 PHE 0.025 0.003 PHE A 189 TRP 0.017 0.002 TRP U 340 HIS 0.011 0.002 HIS W 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.30 (27408) covalent geometry : angle 0.93234 / 0.40 (37951) hydrogen bonds : bond 0.04831 / 3.26 ( 1308) hydrogen bonds : angle 5.56322 / 4.06 ( 3747) metal coordination : bond 0.02302 / 1.28 ( 12) metal coordination : angle 14.10904 / 8.38 ( 36) Misc. bond : bond 0.09244 / 6.96 ( 22) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 667 time to evaluate : 0.806 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 61 TRP cc_start: 0.9356 (p-90) cc_final: 0.9089 (p-90) REVERT: A 90 MET cc_start: 0.9180 (mmm) cc_final: 0.8789 (mmt) REVERT: A 127 ASP cc_start: 0.6361 (OUTLIER) cc_final: 0.6151 (t0) REVERT: A 168 ASN cc_start: 0.8759 (t0) cc_final: 0.8556 (t0) REVERT: A 189 PHE cc_start: 0.7971 (t80) cc_final: 0.7721 (t80) REVERT: A 245 MET cc_start: 0.8654 (mmm) cc_final: 0.8254 (tpp) REVERT: A 303 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7673 (mm110) REVERT: A 315 LYS cc_start: 0.8639 (tptp) cc_final: 0.8173 (mttm) REVERT: A 316 LEU cc_start: 0.8521 (mt) cc_final: 0.8305 (mt) REVERT: A 485 MET cc_start: 0.7958 (tpt) cc_final: 0.7366 (tpp) REVERT: A 495 PHE cc_start: 0.8419 (t80) cc_final: 0.8182 (t80) REVERT: A 521 ASN cc_start: 0.9073 (m-40) cc_final: 0.8761 (m-40) REVERT: A 548 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7671 (mtm) REVERT: A 583 ASP cc_start: 0.7292 (t0) cc_final: 0.6901 (t0) REVERT: A 584 SER cc_start: 0.9003 (t) cc_final: 0.8690 (p) REVERT: A 634 ASP cc_start: 0.8841 (p0) cc_final: 0.8530 (p0) REVERT: A 682 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: A 704 LEU cc_start: 0.7812 (mt) cc_final: 0.7490 (mt) REVERT: a 60 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6604 (tttt) REVERT: a 82 LEU cc_start: 0.8462 (mt) cc_final: 0.8034 (mt) REVERT: a 114 TYR cc_start: 0.8458 (t80) cc_final: 0.7471 (t80) REVERT: a 137 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6499 (mm-30) REVERT: a 165 TRP cc_start: 0.8124 (t-100) cc_final: 0.7799 (t60) REVERT: a 213 MET cc_start: 0.7457 (mtt) cc_final: 0.6990 (mtm) REVERT: a 274 ASP cc_start: 0.7962 (p0) cc_final: 0.7313 (p0) REVERT: a 296 ILE cc_start: 0.8998 (mt) cc_final: 0.8718 (mm) REVERT: a 315 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7379 (tptm) REVERT: a 377 ILE cc_start: 0.8667 (mt) cc_final: 0.8316 (mt) REVERT: a 378 ILE cc_start: 0.9010 (tt) cc_final: 0.8770 (tt) REVERT: a 403 MET cc_start: 0.7383 (tpp) cc_final: 0.5462 (tmm) REVERT: a 411 TRP cc_start: 0.7799 (m100) cc_final: 0.6880 (m-90) REVERT: a 412 ILE cc_start: 0.8139 (mm) cc_final: 0.7869 (mm) REVERT: a 424 ILE cc_start: 0.8357 (mt) cc_final: 0.8117 (mt) REVERT: a 440 TYR cc_start: 0.9008 (t80) cc_final: 0.8792 (t80) REVERT: a 450 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: a 483 TRP cc_start: 0.8155 (t60) cc_final: 0.7672 (t60) REVERT: a 535 THR cc_start: 0.8234 (p) cc_final: 0.7933 (p) REVERT: a 545 TRP cc_start: 0.8771 (m100) cc_final: 0.7769 (m100) REVERT: a 561 TYR cc_start: 0.8620 (t80) cc_final: 0.8366 (t80) REVERT: a 645 GLN cc_start: 0.9102 (mt0) cc_final: 0.8506 (mt0) REVERT: a 646 THR cc_start: 0.8832 (m) cc_final: 0.8318 (p) REVERT: a 700 THR cc_start: 0.7869 (p) cc_final: 0.7665 (t) REVERT: B 160 LYS cc_start: 0.5657 (tptt) cc_final: 0.5365 (ttpt) REVERT: C 47 ARG cc_start: 0.7287 (mmt180) cc_final: 0.6995 (mmm160) REVERT: C 90 MET cc_start: 0.7037 (mtp) cc_final: 0.6646 (mtp) REVERT: c 99 TYR cc_start: 0.6556 (t80) cc_final: 0.5834 (t80) REVERT: c 118 GLU cc_start: 0.5715 (tt0) cc_final: 0.5453 (tt0) REVERT: D 78 TYR cc_start: 0.7306 (m-80) cc_final: 0.7020 (m-80) REVERT: U 31 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7959 (mtmt) REVERT: U 52 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8233 (tttt) REVERT: U 85 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7313 (tt0) REVERT: U 103 MET cc_start: 0.8324 (ttp) cc_final: 0.7895 (tmm) REVERT: U 208 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7669 (pt) REVERT: U 232 MET cc_start: 0.8203 (mtm) cc_final: 0.7952 (ptp) REVERT: U 238 ARG cc_start: 0.8338 (mtp85) cc_final: 0.7562 (mtm-85) REVERT: U 259 ARG cc_start: 0.8673 (ttt90) cc_final: 0.8378 (ttt90) REVERT: U 314 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8033 (ttpt) REVERT: U 325 TYR cc_start: 0.7772 (t80) cc_final: 0.7275 (t80) REVERT: U 361 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7434 (mt-10) REVERT: V 30 VAL cc_start: 0.9006 (t) cc_final: 0.8767 (p) REVERT: V 31 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7918 (mtpp) REVERT: V 35 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7795 (ttpp) REVERT: V 151 LYS cc_start: 0.7763 (mtmt) cc_final: 0.6612 (ttpp) REVERT: V 206 ASN cc_start: 0.7541 (m-40) cc_final: 0.7340 (m-40) REVERT: V 255 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7298 (mm-30) REVERT: V 268 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8681 (tttm) REVERT: V 321 TYR cc_start: 0.8316 (m-10) cc_final: 0.7711 (m-10) REVERT: V 359 GLN cc_start: 0.8017 (tt0) cc_final: 0.7634 (tt0) REVERT: W 33 ARG cc_start: 0.6904 (mmt-90) cc_final: 0.6674 (mmt-90) REVERT: W 64 PHE cc_start: 0.7563 (m-80) cc_final: 0.7037 (m-80) REVERT: W 72 GLU cc_start: 0.7321 (mp0) cc_final: 0.7028 (pm20) REVERT: W 112 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7915 (p) REVERT: W 151 LYS cc_start: 0.7526 (mmtm) cc_final: 0.7289 (mptt) REVERT: W 180 ILE cc_start: 0.8814 (tp) cc_final: 0.8583 (tp) REVERT: W 253 GLN cc_start: 0.7534 (mp-120) cc_final: 0.7219 (mp10) REVERT: W 268 LYS cc_start: 0.7777 (ttmt) cc_final: 0.7237 (pttp) REVERT: W 292 LEU cc_start: 0.8986 (mp) cc_final: 0.8576 (mp) REVERT: W 314 LYS cc_start: 0.7714 (ttmt) cc_final: 0.7050 (tttm) REVERT: W 321 TYR cc_start: 0.7577 (m-80) cc_final: 0.7347 (m-80) REVERT: W 345 TYR cc_start: 0.8958 (t80) cc_final: 0.8692 (t80) outliers start: 108 outliers final: 72 residues processed: 711 average time/residue: 0.1611 time to fit residues: 182.8793 Evaluate side-chains 699 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 620 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 225 TRP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain a residue 60 LYS Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 111 ASN Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 128 THR Chi-restraints excluded: chain a residue 133 THR Chi-restraints excluded: chain a residue 193 VAL Chi-restraints excluded: chain a residue 289 ILE Chi-restraints excluded: chain a residue 409 SER Chi-restraints excluded: chain a residue 413 THR Chi-restraints excluded: chain a residue 420 VAL Chi-restraints excluded: chain a residue 427 THR Chi-restraints excluded: chain a residue 448 ILE Chi-restraints excluded: chain a residue 450 GLU Chi-restraints excluded: chain a residue 473 TRP Chi-restraints excluded: chain a residue 556 SER Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain a residue 626 ILE Chi-restraints excluded: chain a residue 661 VAL Chi-restraints excluded: chain a residue 669 THR Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain c residue 113 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain U residue 15 ASP Chi-restraints excluded: chain U residue 74 ILE Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 127 SER Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain U residue 208 LEU Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain U residue 293 ILE Chi-restraints excluded: chain U residue 317 LEU Chi-restraints excluded: chain U residue 352 VAL Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 191 THR Chi-restraints excluded: chain V residue 210 THR Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 293 ILE Chi-restraints excluded: chain V residue 336 GLU Chi-restraints excluded: chain W residue 18 ILE Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 68 SER Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 136 ASN Chi-restraints excluded: chain W residue 191 THR Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 220 VAL Chi-restraints excluded: chain W residue 288 LEU Chi-restraints excluded: chain W residue 317 LEU Chi-restraints excluded: chain W residue 332 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 252 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 260 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 162 optimal weight: 0.5980 chunk 236 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN a 99 GLN ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN a 406 GLN ** a 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 699 GLN B 166 GLN c 38 ASN c 39 HIS V 156 ASN ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 136 ASN ** W 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.181168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.164379 restraints weight = 36664.766| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.01 r_work: 0.3630 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 27442 Z= 0.183 Angle : 0.940 34.874 37987 Z= 0.343 Chirality : 0.044 0.225 3792 Planarity : 0.005 0.071 4594 Dihedral : 14.813 175.505 4795 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 4.08 % Allowed : 19.56 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2767 helix: 0.86 (0.15), residues: 1147 sheet: -0.46 (0.21), residues: 513 loop : -1.31 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 202 TYR 0.050 0.002 TYR A 321 PHE 0.035 0.002 PHE A 301 TRP 0.035 0.002 TRP a 162 HIS 0.009 0.001 HIS W 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (27408) covalent geometry : angle 0.80874 / 0.34 (37951) hydrogen bonds : bond 0.04226 / 2.84 ( 1308) hydrogen bonds : angle 5.35670 / 3.90 ( 3747) metal coordination : bond 0.01626 / 0.92 ( 12) metal coordination : angle 15.57216 / 9.18 ( 36) Misc. bond : bond 0.02727 / 1.07 ( 22) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 630 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TRP cc_start: 0.9327 (p-90) cc_final: 0.9072 (p-90) REVERT: A 90 MET cc_start: 0.9153 (mmm) cc_final: 0.8690 (mmt) REVERT: A 168 ASN cc_start: 0.8758 (t0) cc_final: 0.8557 (t0) REVERT: A 189 PHE cc_start: 0.7948 (t80) cc_final: 0.7653 (t80) REVERT: A 213 MET cc_start: 0.7914 (mmt) cc_final: 0.7694 (mmt) REVERT: A 245 MET cc_start: 0.8732 (mmm) cc_final: 0.8322 (tpp) REVERT: A 275 MET cc_start: 0.6908 (mmp) cc_final: 0.6582 (mmt) REVERT: A 290 ASN cc_start: 0.9449 (t0) cc_final: 0.9219 (m-40) REVERT: A 303 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7317 (mm110) REVERT: A 315 LYS cc_start: 0.8603 (tptp) cc_final: 0.8123 (mttm) REVERT: A 485 MET cc_start: 0.8007 (tpt) cc_final: 0.7388 (tpp) REVERT: A 521 ASN cc_start: 0.9018 (m-40) cc_final: 0.8727 (m-40) REVERT: A 548 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7613 (mtm) REVERT: A 561 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7841 (t80) REVERT: A 583 ASP cc_start: 0.7283 (t0) cc_final: 0.6895 (t0) REVERT: A 584 SER cc_start: 0.8925 (t) cc_final: 0.8662 (p) REVERT: A 590 HIS cc_start: 0.6854 (m90) cc_final: 0.6555 (m90) REVERT: A 634 ASP cc_start: 0.8809 (p0) cc_final: 0.8476 (p0) REVERT: A 682 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: A 699 GLN cc_start: 0.7585 (tt0) cc_final: 0.6877 (tm-30) REVERT: A 704 LEU cc_start: 0.7820 (mt) cc_final: 0.7512 (mt) REVERT: a 114 TYR cc_start: 0.8430 (t80) cc_final: 0.7372 (t80) REVERT: a 137 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6552 (mm-30) REVERT: a 213 MET cc_start: 0.7313 (mtt) cc_final: 0.6924 (mtm) REVERT: a 242 GLU cc_start: 0.7859 (mt-10) cc_final: 0.6786 (mt-10) REVERT: a 274 ASP cc_start: 0.7840 (p0) cc_final: 0.7170 (p0) REVERT: a 275 MET cc_start: 0.8211 (tpt) cc_final: 0.6786 (mtm) REVERT: a 296 ILE cc_start: 0.8931 (mt) cc_final: 0.8617 (mm) REVERT: a 315 LYS cc_start: 0.7769 (mmtt) cc_final: 0.7230 (tptm) REVERT: a 327 ARG cc_start: 0.6604 (mtp85) cc_final: 0.6396 (mtt180) REVERT: a 355 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8048 (mp) REVERT: a 364 MET cc_start: 0.7975 (tpp) cc_final: 0.7656 (tpp) REVERT: a 377 ILE cc_start: 0.8502 (mt) cc_final: 0.8204 (mt) REVERT: a 378 ILE cc_start: 0.8949 (tt) cc_final: 0.8735 (tt) REVERT: a 401 ASN cc_start: 0.6827 (m-40) cc_final: 0.6622 (t0) REVERT: a 403 MET cc_start: 0.7285 (tpp) cc_final: 0.5419 (tmm) REVERT: a 411 TRP cc_start: 0.7651 (m100) cc_final: 0.6826 (m-90) REVERT: a 412 ILE cc_start: 0.8059 (mm) cc_final: 0.7823 (mm) REVERT: a 424 ILE cc_start: 0.8307 (mt) cc_final: 0.8078 (mt) REVERT: a 440 TYR cc_start: 0.9015 (t80) cc_final: 0.8628 (t80) REVERT: a 450 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: a 483 TRP cc_start: 0.8113 (t60) cc_final: 0.7661 (t60) REVERT: a 535 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7738 (p) REVERT: a 545 TRP cc_start: 0.8695 (m100) cc_final: 0.7463 (m100) REVERT: a 561 TYR cc_start: 0.8538 (t80) cc_final: 0.8285 (t80) REVERT: a 645 GLN cc_start: 0.9053 (mt0) cc_final: 0.8450 (mt0) REVERT: a 646 THR cc_start: 0.8809 (m) cc_final: 0.8274 (p) REVERT: B 160 LYS cc_start: 0.5486 (tptt) cc_final: 0.5255 (ttpt) REVERT: C 34 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7737 (tp) REVERT: C 47 ARG cc_start: 0.7246 (mmt180) cc_final: 0.6935 (mmm160) REVERT: C 90 MET cc_start: 0.6941 (mtp) cc_final: 0.6590 (mtp) REVERT: c 97 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.6202 (mmm-85) REVERT: c 99 TYR cc_start: 0.6702 (t80) cc_final: 0.6036 (t80) REVERT: c 118 GLU cc_start: 0.5694 (tt0) cc_final: 0.5331 (tt0) REVERT: D 88 ILE cc_start: 0.4228 (OUTLIER) cc_final: 0.3915 (pt) REVERT: U 17 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7687 (tt0) REVERT: U 31 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7874 (mtmt) REVERT: U 52 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8138 (tttt) REVERT: U 85 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7495 (tt0) REVERT: U 103 MET cc_start: 0.8226 (ttp) cc_final: 0.7875 (tmm) REVERT: U 204 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7449 (tt0) REVERT: U 208 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7650 (pt) REVERT: U 238 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7481 (mtm-85) REVERT: U 314 LYS cc_start: 0.8392 (ttpt) cc_final: 0.7971 (ttpt) REVERT: U 325 TYR cc_start: 0.7962 (t80) cc_final: 0.7740 (t80) REVERT: V 30 VAL cc_start: 0.8973 (t) cc_final: 0.8702 (p) REVERT: V 31 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7334 (mttt) REVERT: V 35 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7724 (ttpp) REVERT: V 255 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7277 (mm-30) REVERT: V 268 LYS cc_start: 0.8909 (ttmt) cc_final: 0.8643 (tttm) REVERT: V 321 TYR cc_start: 0.8279 (m-10) cc_final: 0.7621 (m-10) REVERT: W 64 PHE cc_start: 0.7406 (m-80) cc_final: 0.6757 (m-80) REVERT: W 112 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7923 (p) REVERT: W 180 ILE cc_start: 0.8766 (tp) cc_final: 0.8546 (tp) REVERT: W 253 GLN cc_start: 0.7408 (mp-120) cc_final: 0.7108 (mp10) REVERT: W 268 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7197 (pttp) REVERT: W 292 LEU cc_start: 0.8845 (mp) cc_final: 0.8502 (mp) REVERT: W 314 LYS cc_start: 0.7679 (ttmt) cc_final: 0.7011 (tttm) REVERT: W 319 LYS cc_start: 0.7405 (tptp) cc_final: 0.7122 (mptt) REVERT: W 321 TYR cc_start: 0.7407 (m-80) cc_final: 0.7092 (m-80) outliers start: 95 outliers final: 60 residues processed: 674 average time/residue: 0.1638 time to fit residues: 176.6693 Evaluate side-chains 672 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 601 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 225 TRP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 561 TYR Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 128 THR Chi-restraints excluded: chain a residue 158 ILE Chi-restraints excluded: chain a residue 289 ILE Chi-restraints excluded: chain a residue 355 LEU Chi-restraints excluded: chain a residue 395 LEU Chi-restraints excluded: chain a residue 420 VAL Chi-restraints excluded: chain a residue 450 GLU Chi-restraints excluded: chain a residue 473 TRP Chi-restraints excluded: chain a residue 528 LEU Chi-restraints excluded: chain a residue 535 THR Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain a residue 626 ILE Chi-restraints excluded: chain a residue 661 VAL Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain c residue 97 ARG Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 74 ILE Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 127 SER Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain U residue 208 LEU Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 170 ILE Chi-restraints excluded: chain V residue 210 THR Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 336 GLU Chi-restraints excluded: chain W residue 18 ILE Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 191 THR Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 224 ARG Chi-restraints excluded: chain W residue 288 LEU Chi-restraints excluded: chain W residue 317 LEU Chi-restraints excluded: chain W residue 332 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 270 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 178 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN a 406 GLN a 418 GLN ** a 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 ASN V 156 ASN ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.178650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.161967 restraints weight = 36663.286| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.98 r_work: 0.3688 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 27442 Z= 0.214 Angle : 0.955 36.293 37987 Z= 0.348 Chirality : 0.045 0.233 3792 Planarity : 0.005 0.071 4594 Dihedral : 14.496 175.209 4795 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.80 % Allowed : 20.76 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 2767 helix: 0.86 (0.15), residues: 1157 sheet: -0.41 (0.22), residues: 509 loop : -1.31 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 114 TYR 0.047 0.002 TYR A 321 PHE 0.041 0.002 PHE A 301 TRP 0.032 0.002 TRP a 162 HIS 0.010 0.001 HIS W 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (27408) covalent geometry : angle 0.81805 / 0.35 (37951) hydrogen bonds : bond 0.04258 / 2.87 ( 1308) hydrogen bonds : angle 5.34799 / 3.89 ( 3747) metal coordination : bond 0.01703 / 0.96 ( 12) metal coordination : angle 15.99828 / 9.40 ( 36) Misc. bond : bond 0.03123 / 1.24 ( 22) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 629 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TRP cc_start: 0.9315 (p-90) cc_final: 0.9102 (p-90) REVERT: A 90 MET cc_start: 0.9128 (mmm) cc_final: 0.8651 (mmt) REVERT: A 168 ASN cc_start: 0.8761 (t0) cc_final: 0.8513 (t0) REVERT: A 213 MET cc_start: 0.7820 (mmt) cc_final: 0.7601 (mmt) REVERT: A 245 MET cc_start: 0.8727 (mmm) cc_final: 0.8318 (tpp) REVERT: A 275 MET cc_start: 0.6923 (mmp) cc_final: 0.6535 (mmt) REVERT: A 290 ASN cc_start: 0.9491 (t0) cc_final: 0.9206 (m-40) REVERT: A 303 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7337 (mm-40) REVERT: A 315 LYS cc_start: 0.8571 (tptp) cc_final: 0.8117 (mttm) REVERT: A 319 TYR cc_start: 0.8710 (m-80) cc_final: 0.8448 (m-80) REVERT: A 344 LYS cc_start: 0.6867 (pttt) cc_final: 0.6459 (pttt) REVERT: A 477 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6769 (p0) REVERT: A 485 MET cc_start: 0.8082 (tpt) cc_final: 0.7460 (tpp) REVERT: A 521 ASN cc_start: 0.9028 (m-40) cc_final: 0.8757 (m-40) REVERT: A 548 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7613 (mtm) REVERT: A 583 ASP cc_start: 0.7209 (t0) cc_final: 0.6776 (t0) REVERT: A 634 ASP cc_start: 0.8727 (p0) cc_final: 0.8472 (p0) REVERT: A 674 LYS cc_start: 0.8153 (mttt) cc_final: 0.7560 (mtmm) REVERT: A 682 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: A 704 LEU cc_start: 0.7776 (mt) cc_final: 0.7465 (mt) REVERT: a 60 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6653 (tttt) REVERT: a 74 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7468 (mm-40) REVERT: a 99 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7447 (tp-100) REVERT: a 114 TYR cc_start: 0.8466 (t80) cc_final: 0.7419 (t80) REVERT: a 137 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6584 (mm-30) REVERT: a 162 TRP cc_start: 0.7711 (t-100) cc_final: 0.7418 (t-100) REVERT: a 213 MET cc_start: 0.7283 (mtt) cc_final: 0.6908 (mtm) REVERT: a 218 LEU cc_start: 0.7396 (tp) cc_final: 0.7051 (mm) REVERT: a 274 ASP cc_start: 0.7887 (p0) cc_final: 0.7139 (p0) REVERT: a 275 MET cc_start: 0.8194 (tpt) cc_final: 0.6869 (mtm) REVERT: a 296 ILE cc_start: 0.8931 (mt) cc_final: 0.8650 (mm) REVERT: a 315 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7246 (tptm) REVERT: a 327 ARG cc_start: 0.6840 (mtp85) cc_final: 0.6616 (mtt180) REVERT: a 355 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8173 (mp) REVERT: a 364 MET cc_start: 0.7978 (tpp) cc_final: 0.7689 (tpp) REVERT: a 377 ILE cc_start: 0.8608 (mt) cc_final: 0.8302 (mt) REVERT: a 378 ILE cc_start: 0.8974 (tt) cc_final: 0.8745 (tt) REVERT: a 401 ASN cc_start: 0.6883 (m-40) cc_final: 0.6576 (t0) REVERT: a 403 MET cc_start: 0.7359 (tpp) cc_final: 0.5588 (tmm) REVERT: a 411 TRP cc_start: 0.7609 (m100) cc_final: 0.6803 (m-90) REVERT: a 412 ILE cc_start: 0.8081 (mm) cc_final: 0.7859 (mm) REVERT: a 424 ILE cc_start: 0.8367 (mt) cc_final: 0.8134 (mt) REVERT: a 440 TYR cc_start: 0.9034 (t80) cc_final: 0.8666 (t80) REVERT: a 483 TRP cc_start: 0.8097 (t60) cc_final: 0.7765 (t60) REVERT: a 535 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7758 (p) REVERT: a 545 TRP cc_start: 0.8743 (m100) cc_final: 0.7514 (m100) REVERT: a 561 TYR cc_start: 0.8562 (t80) cc_final: 0.8324 (t80) REVERT: a 625 PHE cc_start: 0.8649 (p90) cc_final: 0.8342 (p90) REVERT: a 645 GLN cc_start: 0.9086 (mt0) cc_final: 0.8493 (mt0) REVERT: a 646 THR cc_start: 0.8827 (m) cc_final: 0.8296 (p) REVERT: a 678 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8437 (m) REVERT: C 34 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7710 (tp) REVERT: C 47 ARG cc_start: 0.7232 (mmt180) cc_final: 0.6885 (mmm160) REVERT: C 50 MET cc_start: 0.6355 (tmm) cc_final: 0.6091 (tmm) REVERT: C 64 MET cc_start: 0.6761 (mtm) cc_final: 0.6428 (mtp) REVERT: C 90 MET cc_start: 0.7000 (mtp) cc_final: 0.6673 (mtp) REVERT: c 97 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6235 (mmm-85) REVERT: c 118 GLU cc_start: 0.5559 (tt0) cc_final: 0.5233 (tt0) REVERT: D 88 ILE cc_start: 0.4374 (OUTLIER) cc_final: 0.4082 (pt) REVERT: U 85 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7416 (tt0) REVERT: U 103 MET cc_start: 0.8255 (ttp) cc_final: 0.7971 (tmm) REVERT: U 185 PHE cc_start: 0.7250 (m-80) cc_final: 0.7005 (m-80) REVERT: U 208 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7676 (pt) REVERT: U 238 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7437 (mtm-85) REVERT: U 253 GLN cc_start: 0.7837 (pm20) cc_final: 0.7603 (pm20) REVERT: U 314 LYS cc_start: 0.8512 (ttpt) cc_final: 0.8274 (ttmt) REVERT: U 338 TYR cc_start: 0.7911 (m-80) cc_final: 0.7636 (m-10) REVERT: V 30 VAL cc_start: 0.8988 (t) cc_final: 0.8747 (p) REVERT: V 31 LYS cc_start: 0.8205 (mttt) cc_final: 0.7412 (mttt) REVERT: V 35 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7795 (ttpp) REVERT: V 206 ASN cc_start: 0.7515 (m-40) cc_final: 0.7288 (m-40) REVERT: V 255 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7223 (mm-30) REVERT: V 295 LEU cc_start: 0.8860 (mt) cc_final: 0.8635 (mt) REVERT: V 321 TYR cc_start: 0.8196 (m-10) cc_final: 0.7572 (m-10) REVERT: W 50 ASP cc_start: 0.7166 (t0) cc_final: 0.6378 (p0) REVERT: W 64 PHE cc_start: 0.7273 (m-80) cc_final: 0.6579 (m-80) REVERT: W 180 ILE cc_start: 0.8752 (tp) cc_final: 0.8534 (tp) REVERT: W 268 LYS cc_start: 0.7727 (ttmt) cc_final: 0.7298 (pttp) REVERT: W 292 LEU cc_start: 0.8889 (mp) cc_final: 0.8577 (mp) outliers start: 112 outliers final: 80 residues processed: 684 average time/residue: 0.1642 time to fit residues: 180.4808 Evaluate side-chains 693 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 602 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 225 TRP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain a residue 60 LYS Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 111 ASN Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 128 THR Chi-restraints excluded: chain a residue 158 ILE Chi-restraints excluded: chain a residue 193 VAL Chi-restraints excluded: chain a residue 197 THR Chi-restraints excluded: chain a residue 238 THR Chi-restraints excluded: chain a residue 289 ILE Chi-restraints excluded: chain a residue 355 LEU Chi-restraints excluded: chain a residue 381 VAL Chi-restraints excluded: chain a residue 395 LEU Chi-restraints excluded: chain a residue 409 SER Chi-restraints excluded: chain a residue 420 VAL Chi-restraints excluded: chain a residue 450 GLU Chi-restraints excluded: chain a residue 473 TRP Chi-restraints excluded: chain a residue 528 LEU Chi-restraints excluded: chain a residue 535 THR Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain a residue 626 ILE Chi-restraints excluded: chain a residue 661 VAL Chi-restraints excluded: chain a residue 669 THR Chi-restraints excluded: chain a residue 678 THR Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 97 ARG Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 110 SER Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 127 SER Chi-restraints excluded: chain U residue 158 ASP Chi-restraints excluded: chain U residue 208 LEU Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain U residue 293 ILE Chi-restraints excluded: chain U residue 323 ILE Chi-restraints excluded: chain V residue 82 LEU Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 191 THR Chi-restraints excluded: chain V residue 210 THR Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 288 LEU Chi-restraints excluded: chain V residue 293 ILE Chi-restraints excluded: chain V residue 336 GLU Chi-restraints excluded: chain W residue 18 ILE Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 133 ASN Chi-restraints excluded: chain W residue 191 THR Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 201 SER Chi-restraints excluded: chain W residue 224 ARG Chi-restraints excluded: chain W residue 288 LEU Chi-restraints excluded: chain W residue 317 LEU Chi-restraints excluded: chain W residue 332 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 168 optimal weight: 0.4980 chunk 241 optimal weight: 7.9990 chunk 198 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 chunk 193 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 GLN A 645 GLN a 406 GLN ** a 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 289 ASN V 54 ASN V 156 ASN ** V 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.183300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.166687 restraints weight = 36475.449| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.02 r_work: 0.3690 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 27442 Z= 0.147 Angle : 0.893 34.373 37987 Z= 0.326 Chirality : 0.043 0.211 3792 Planarity : 0.005 0.069 4594 Dihedral : 14.175 174.804 4795 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.29 % Allowed : 22.14 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2767 helix: 1.13 (0.15), residues: 1149 sheet: -0.40 (0.22), residues: 509 loop : -1.18 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 224 TYR 0.041 0.002 TYR A 321 PHE 0.050 0.002 PHE A 301 TRP 0.022 0.001 TRP A 464 HIS 0.011 0.001 HIS W 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (27408) covalent geometry : angle 0.76235 / 0.32 (37951) hydrogen bonds : bond 0.03950 / 2.65 ( 1308) hydrogen bonds : angle 5.17096 / 3.76 ( 3747) metal coordination : bond 0.01284 / 0.82 ( 12) metal coordination : angle 15.15457 / 9.26 ( 36) Misc. bond : bond 0.02203 / 0.79 ( 22) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 639 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TRP cc_start: 0.9226 (p-90) cc_final: 0.8954 (p-90) REVERT: A 90 MET cc_start: 0.9148 (mmm) cc_final: 0.8662 (mmt) REVERT: A 130 SER cc_start: 0.8618 (t) cc_final: 0.8355 (m) REVERT: A 168 ASN cc_start: 0.8735 (t0) cc_final: 0.8473 (t0) REVERT: A 213 MET cc_start: 0.7926 (mmt) cc_final: 0.7031 (mmt) REVERT: A 245 MET cc_start: 0.8728 (mmm) cc_final: 0.8274 (tpp) REVERT: A 275 MET cc_start: 0.6873 (mmp) cc_final: 0.6557 (mmt) REVERT: A 303 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7272 (mm-40) REVERT: A 315 LYS cc_start: 0.8524 (tptp) cc_final: 0.8042 (mttm) REVERT: A 344 LYS cc_start: 0.6851 (pttt) cc_final: 0.6408 (pttt) REVERT: A 408 LYS cc_start: 0.8057 (tppp) cc_final: 0.7854 (tppp) REVERT: A 485 MET cc_start: 0.8132 (tpt) cc_final: 0.7694 (tpt) REVERT: A 519 LYS cc_start: 0.7614 (pttt) cc_final: 0.6822 (ptmt) REVERT: A 521 ASN cc_start: 0.8999 (m-40) cc_final: 0.8761 (m-40) REVERT: A 583 ASP cc_start: 0.7327 (t0) cc_final: 0.6814 (t0) REVERT: A 594 SER cc_start: 0.8641 (p) cc_final: 0.8327 (p) REVERT: A 634 ASP cc_start: 0.8675 (p0) cc_final: 0.8450 (p0) REVERT: A 664 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7210 (ttm170) REVERT: A 674 LYS cc_start: 0.8071 (mttt) cc_final: 0.7616 (mtmm) REVERT: A 704 LEU cc_start: 0.7728 (mt) cc_final: 0.7404 (mt) REVERT: a 60 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6498 (tttt) REVERT: a 137 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6569 (mm-30) REVERT: a 162 TRP cc_start: 0.7657 (t-100) cc_final: 0.7388 (t-100) REVERT: a 213 MET cc_start: 0.7254 (mtt) cc_final: 0.6867 (mtm) REVERT: a 218 LEU cc_start: 0.7280 (tp) cc_final: 0.6959 (mm) REVERT: a 237 GLN cc_start: 0.7889 (mp10) cc_final: 0.7640 (mp10) REVERT: a 242 GLU cc_start: 0.7766 (mt-10) cc_final: 0.6511 (mt-10) REVERT: a 274 ASP cc_start: 0.7640 (p0) cc_final: 0.6869 (p0) REVERT: a 275 MET cc_start: 0.8091 (tpt) cc_final: 0.6906 (mtm) REVERT: a 296 ILE cc_start: 0.8883 (mt) cc_final: 0.8560 (mm) REVERT: a 315 LYS cc_start: 0.7563 (mmtt) cc_final: 0.7120 (tptm) REVERT: a 327 ARG cc_start: 0.6622 (mtp85) cc_final: 0.6405 (mtt180) REVERT: a 377 ILE cc_start: 0.8461 (mt) cc_final: 0.8168 (mt) REVERT: a 378 ILE cc_start: 0.8926 (tt) cc_final: 0.8694 (tt) REVERT: a 401 ASN cc_start: 0.6730 (m-40) cc_final: 0.6478 (t0) REVERT: a 403 MET cc_start: 0.7198 (tpp) cc_final: 0.5330 (tmm) REVERT: a 411 TRP cc_start: 0.7453 (m100) cc_final: 0.6685 (m-90) REVERT: a 424 ILE cc_start: 0.8338 (mt) cc_final: 0.8094 (mt) REVERT: a 429 MET cc_start: 0.6904 (mtt) cc_final: 0.6671 (ttt) REVERT: a 483 TRP cc_start: 0.8062 (t60) cc_final: 0.7727 (t60) REVERT: a 535 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7590 (p) REVERT: a 545 TRP cc_start: 0.8707 (m100) cc_final: 0.7441 (m100) REVERT: a 561 TYR cc_start: 0.8400 (t80) cc_final: 0.8098 (t80) REVERT: a 625 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8333 (p90) REVERT: a 645 GLN cc_start: 0.9023 (mt0) cc_final: 0.8448 (mt0) REVERT: a 646 THR cc_start: 0.8822 (m) cc_final: 0.8296 (p) REVERT: a 678 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8384 (m) REVERT: C 34 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7727 (tp) REVERT: C 47 ARG cc_start: 0.7234 (mmt180) cc_final: 0.6841 (mmm160) REVERT: C 64 MET cc_start: 0.6879 (mtm) cc_final: 0.6606 (mtp) REVERT: C 90 MET cc_start: 0.6647 (mtp) cc_final: 0.6297 (mtp) REVERT: c 97 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.5701 (mmm-85) REVERT: c 118 GLU cc_start: 0.5530 (tt0) cc_final: 0.5176 (tt0) REVERT: D 88 ILE cc_start: 0.4281 (OUTLIER) cc_final: 0.3986 (pt) REVERT: D 114 MET cc_start: 0.6232 (ptp) cc_final: 0.5638 (ptp) REVERT: U 17 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7758 (tt0) REVERT: U 85 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7421 (tt0) REVERT: U 103 MET cc_start: 0.8173 (ttp) cc_final: 0.7896 (tmm) REVERT: U 140 MET cc_start: 0.7941 (mmm) cc_final: 0.7208 (mtt) REVERT: U 208 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7539 (pt) REVERT: U 314 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8174 (ttmt) REVERT: U 357 VAL cc_start: 0.7487 (OUTLIER) cc_final: 0.7225 (m) REVERT: V 30 VAL cc_start: 0.9013 (t) cc_final: 0.8806 (p) REVERT: V 31 LYS cc_start: 0.8107 (mttt) cc_final: 0.7230 (mttt) REVERT: V 35 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7730 (ttpp) REVERT: V 255 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7263 (mm-30) REVERT: V 321 TYR cc_start: 0.8222 (m-10) cc_final: 0.7622 (m-10) REVERT: W 64 PHE cc_start: 0.7339 (m-80) cc_final: 0.6610 (m-80) REVERT: W 66 ARG cc_start: 0.6904 (ttp-170) cc_final: 0.6589 (ttm170) REVERT: W 103 MET cc_start: 0.7329 (ppp) cc_final: 0.6937 (ppp) REVERT: W 104 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7754 (t) REVERT: W 180 ILE cc_start: 0.8749 (tp) cc_final: 0.8510 (tp) REVERT: W 268 LYS cc_start: 0.7655 (ttmt) cc_final: 0.7299 (pttp) REVERT: W 292 LEU cc_start: 0.8875 (mp) cc_final: 0.8589 (mp) REVERT: W 314 LYS cc_start: 0.7646 (ttmt) cc_final: 0.6893 (ttpt) REVERT: W 319 LYS cc_start: 0.7478 (tptp) cc_final: 0.7254 (mptt) outliers start: 100 outliers final: 63 residues processed: 690 average time/residue: 0.1645 time to fit residues: 182.3732 Evaluate side-chains 690 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 617 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 225 TRP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain a residue 60 LYS Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 128 THR Chi-restraints excluded: chain a residue 158 ILE Chi-restraints excluded: chain a residue 289 ILE Chi-restraints excluded: chain a residue 395 LEU Chi-restraints excluded: chain a residue 409 SER Chi-restraints excluded: chain a residue 473 TRP Chi-restraints excluded: chain a residue 528 LEU Chi-restraints excluded: chain a residue 535 THR Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain a residue 625 PHE Chi-restraints excluded: chain a residue 626 ILE Chi-restraints excluded: chain a residue 661 VAL Chi-restraints excluded: chain a residue 678 THR Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain c residue 97 ARG Chi-restraints excluded: chain c residue 101 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 127 SER Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain U residue 158 ASP Chi-restraints excluded: chain U residue 208 LEU Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain U residue 313 LEU Chi-restraints excluded: chain U residue 317 LEU Chi-restraints excluded: chain U residue 357 VAL Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 191 THR Chi-restraints excluded: chain V residue 209 ASN Chi-restraints excluded: chain V residue 210 THR Chi-restraints excluded: chain V residue 288 LEU Chi-restraints excluded: chain V residue 293 ILE Chi-restraints excluded: chain W residue 18 ILE Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 191 THR Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 201 SER Chi-restraints excluded: chain W residue 288 LEU Chi-restraints excluded: chain W residue 317 LEU Chi-restraints excluded: chain W residue 332 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 114 optimal weight: 0.0170 chunk 88 optimal weight: 4.9990 chunk 226 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN a 406 GLN ** a 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 699 GLN V 156 ASN ** V 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.182705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.165914 restraints weight = 36579.759| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.04 r_work: 0.3651 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 27442 Z= 0.160 Angle : 0.898 35.784 37987 Z= 0.331 Chirality : 0.044 0.263 3792 Planarity : 0.005 0.054 4594 Dihedral : 14.061 175.357 4795 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.03 % Allowed : 23.38 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2767 helix: 1.15 (0.15), residues: 1148 sheet: -0.34 (0.22), residues: 506 loop : -1.17 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 224 TYR 0.039 0.002 TYR A 561 PHE 0.055 0.002 PHE A 301 TRP 0.035 0.002 TRP W 27 HIS 0.010 0.001 HIS W 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (27408) covalent geometry : angle 0.77195 / 0.33 (37951) hydrogen bonds : bond 0.03961 / 2.65 ( 1308) hydrogen bonds : angle 5.16016 / 3.76 ( 3747) metal coordination : bond 0.01211 / 0.72 ( 12) metal coordination : angle 14.89551 / 8.97 ( 36) Misc. bond : bond 0.01941 / 0.74 ( 22) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 607 time to evaluate : 0.862 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 61 TRP cc_start: 0.9251 (p-90) cc_final: 0.8968 (p-90) REVERT: A 90 MET cc_start: 0.9162 (mmm) cc_final: 0.8670 (mmt) REVERT: A 130 SER cc_start: 0.8700 (t) cc_final: 0.8446 (m) REVERT: A 168 ASN cc_start: 0.8730 (t0) cc_final: 0.8461 (t0) REVERT: A 212 TYR cc_start: 0.8765 (t80) cc_final: 0.8502 (t80) REVERT: A 213 MET cc_start: 0.8027 (mmt) cc_final: 0.7804 (mmt) REVERT: A 245 MET cc_start: 0.8736 (mmm) cc_final: 0.8269 (tpp) REVERT: A 275 MET cc_start: 0.7004 (mmp) cc_final: 0.6581 (mmt) REVERT: A 303 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7190 (mm110) REVERT: A 315 LYS cc_start: 0.8507 (tptp) cc_final: 0.8019 (mttm) REVERT: A 344 LYS cc_start: 0.6878 (pttt) cc_final: 0.6393 (pttt) REVERT: A 485 MET cc_start: 0.8103 (tpt) cc_final: 0.7807 (tpt) REVERT: A 548 MET cc_start: 0.7601 (mtm) cc_final: 0.7301 (mtm) REVERT: A 583 ASP cc_start: 0.7409 (t0) cc_final: 0.6855 (t0) REVERT: A 594 SER cc_start: 0.8702 (p) cc_final: 0.8373 (p) REVERT: A 704 LEU cc_start: 0.7766 (mt) cc_final: 0.7415 (mt) REVERT: a 60 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6697 (tttt) REVERT: a 99 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7338 (tp40) REVERT: a 114 TYR cc_start: 0.8459 (t80) cc_final: 0.8226 (t80) REVERT: a 137 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6566 (mm-30) REVERT: a 213 MET cc_start: 0.7336 (mtt) cc_final: 0.6939 (mtm) REVERT: a 218 LEU cc_start: 0.7185 (tp) cc_final: 0.6879 (mm) REVERT: a 274 ASP cc_start: 0.7640 (p0) cc_final: 0.6883 (p0) REVERT: a 296 ILE cc_start: 0.8889 (mt) cc_final: 0.8561 (mm) REVERT: a 315 LYS cc_start: 0.7566 (mmtt) cc_final: 0.6998 (tptm) REVERT: a 327 ARG cc_start: 0.6748 (mtp85) cc_final: 0.6543 (mtt180) REVERT: a 377 ILE cc_start: 0.8496 (mt) cc_final: 0.8212 (mt) REVERT: a 378 ILE cc_start: 0.8898 (tt) cc_final: 0.8669 (tt) REVERT: a 401 ASN cc_start: 0.6822 (m-40) cc_final: 0.6524 (t0) REVERT: a 403 MET cc_start: 0.7224 (tpp) cc_final: 0.5213 (tmm) REVERT: a 411 TRP cc_start: 0.7545 (m100) cc_final: 0.6705 (m-90) REVERT: a 424 ILE cc_start: 0.8318 (mt) cc_final: 0.8086 (mt) REVERT: a 440 TYR cc_start: 0.8959 (t80) cc_final: 0.8517 (t80) REVERT: a 482 ASP cc_start: 0.8100 (m-30) cc_final: 0.7551 (m-30) REVERT: a 483 TRP cc_start: 0.8101 (t60) cc_final: 0.7770 (t60) REVERT: a 545 TRP cc_start: 0.8739 (m100) cc_final: 0.7628 (m100) REVERT: a 561 TYR cc_start: 0.8488 (t80) cc_final: 0.7894 (t80) REVERT: a 625 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8468 (p90) REVERT: a 645 GLN cc_start: 0.9032 (mt0) cc_final: 0.8458 (mt0) REVERT: a 646 THR cc_start: 0.8864 (m) cc_final: 0.8353 (p) REVERT: a 678 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8556 (m) REVERT: C 34 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7663 (tp) REVERT: C 47 ARG cc_start: 0.7174 (mmt180) cc_final: 0.6869 (mmm160) REVERT: C 64 MET cc_start: 0.6879 (mtm) cc_final: 0.6614 (mtp) REVERT: C 90 MET cc_start: 0.6608 (mtp) cc_final: 0.6266 (mtp) REVERT: c 97 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.5539 (mmm-85) REVERT: c 118 GLU cc_start: 0.5685 (tt0) cc_final: 0.5298 (tt0) REVERT: D 88 ILE cc_start: 0.4234 (OUTLIER) cc_final: 0.3958 (pt) REVERT: U 17 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7748 (tt0) REVERT: U 85 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7428 (tt0) REVERT: U 103 MET cc_start: 0.8167 (ttp) cc_final: 0.7932 (tmm) REVERT: U 140 MET cc_start: 0.7991 (mmm) cc_final: 0.7186 (mtt) REVERT: U 208 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7487 (pt) REVERT: U 314 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8304 (ttmt) REVERT: U 338 TYR cc_start: 0.7598 (m-10) cc_final: 0.7392 (m-10) REVERT: U 357 VAL cc_start: 0.7586 (OUTLIER) cc_final: 0.7339 (m) REVERT: V 30 VAL cc_start: 0.9003 (t) cc_final: 0.8799 (p) REVERT: V 31 LYS cc_start: 0.8107 (mttt) cc_final: 0.7209 (mttt) REVERT: V 35 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7684 (ttpp) REVERT: V 161 ASP cc_start: 0.7649 (t70) cc_final: 0.7206 (t0) REVERT: V 255 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7322 (mm-30) REVERT: V 321 TYR cc_start: 0.8293 (m-10) cc_final: 0.7673 (m-10) REVERT: W 64 PHE cc_start: 0.7372 (m-80) cc_final: 0.6597 (m-80) REVERT: W 66 ARG cc_start: 0.6900 (ttp-170) cc_final: 0.6542 (ttm170) REVERT: W 103 MET cc_start: 0.7248 (ppp) cc_final: 0.6831 (ppp) REVERT: W 104 VAL cc_start: 0.7882 (OUTLIER) cc_final: 0.7666 (t) REVERT: W 180 ILE cc_start: 0.8769 (tp) cc_final: 0.8527 (tp) REVERT: W 268 LYS cc_start: 0.7641 (ttmt) cc_final: 0.7264 (pttp) REVERT: W 319 LYS cc_start: 0.7505 (tptp) cc_final: 0.7258 (mptt) outliers start: 94 outliers final: 67 residues processed: 656 average time/residue: 0.1681 time to fit residues: 177.5823 Evaluate side-chains 670 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 594 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 225 TRP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain a residue 60 LYS Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 128 THR Chi-restraints excluded: chain a residue 158 ILE Chi-restraints excluded: chain a residue 289 ILE Chi-restraints excluded: chain a residue 395 LEU Chi-restraints excluded: chain a residue 409 SER Chi-restraints excluded: chain a residue 473 TRP Chi-restraints excluded: chain a residue 528 LEU Chi-restraints excluded: chain a residue 535 THR Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 574 VAL Chi-restraints excluded: chain a residue 625 PHE Chi-restraints excluded: chain a residue 626 ILE Chi-restraints excluded: chain a residue 661 VAL Chi-restraints excluded: chain a residue 678 THR Chi-restraints excluded: chain a residue 682 PHE Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 97 ARG Chi-restraints excluded: chain c residue 101 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 127 SER Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain U residue 208 LEU Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain U residue 317 LEU Chi-restraints excluded: chain U residue 323 ILE Chi-restraints excluded: chain U residue 357 VAL Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 191 THR Chi-restraints excluded: chain V residue 210 THR Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 288 LEU Chi-restraints excluded: chain V residue 293 ILE Chi-restraints excluded: chain V residue 336 GLU Chi-restraints excluded: chain W residue 18 ILE Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 87 ASP Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 136 ASN Chi-restraints excluded: chain W residue 191 THR Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 201 SER Chi-restraints excluded: chain W residue 224 ARG Chi-restraints excluded: chain W residue 288 LEU Chi-restraints excluded: chain W residue 317 LEU Chi-restraints excluded: chain W residue 332 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 99 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 136 optimal weight: 0.0270 chunk 140 optimal weight: 0.0470 chunk 161 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 166 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 156 ASN W 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.186725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.170195 restraints weight = 36391.703| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.03 r_work: 0.3697 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27442 Z= 0.132 Angle : 0.873 39.829 37987 Z= 0.322 Chirality : 0.043 0.208 3792 Planarity : 0.004 0.056 4594 Dihedral : 13.916 175.736 4795 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.60 % Allowed : 24.11 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2767 helix: 1.24 (0.15), residues: 1147 sheet: -0.33 (0.22), residues: 501 loop : -1.10 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 224 TYR 0.032 0.002 TYR A 561 PHE 0.059 0.002 PHE A 301 TRP 0.036 0.002 TRP a 165 HIS 0.010 0.001 HIS U 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (27408) covalent geometry : angle 0.74627 / 0.32 (37951) hydrogen bonds : bond 0.03818 / 2.54 ( 1308) hydrogen bonds : angle 5.03788 / 3.67 ( 3747) metal coordination : bond 0.00912 / 0.57 ( 12) metal coordination : angle 14.71950 / 8.80 ( 36) Misc. bond : bond 0.01400 / 0.72 ( 22) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 621 time to evaluate : 0.831 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 61 TRP cc_start: 0.9215 (p-90) cc_final: 0.8883 (p-90) REVERT: A 90 MET cc_start: 0.9151 (mmm) cc_final: 0.8649 (mmt) REVERT: A 130 SER cc_start: 0.8616 (t) cc_final: 0.8388 (m) REVERT: A 212 TYR cc_start: 0.8739 (t80) cc_final: 0.8439 (t80) REVERT: A 245 MET cc_start: 0.8640 (mmm) cc_final: 0.8196 (tpp) REVERT: A 275 MET cc_start: 0.6958 (mmp) cc_final: 0.6613 (mmt) REVERT: A 303 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7206 (mm-40) REVERT: A 315 LYS cc_start: 0.8421 (tptp) cc_final: 0.7884 (mttm) REVERT: A 344 LYS cc_start: 0.6821 (pttt) cc_final: 0.6063 (mttt) REVERT: A 408 LYS cc_start: 0.7950 (tppp) cc_final: 0.7736 (tppp) REVERT: A 495 PHE cc_start: 0.8189 (t80) cc_final: 0.7909 (t80) REVERT: A 548 MET cc_start: 0.7563 (mtm) cc_final: 0.7285 (mtm) REVERT: A 583 ASP cc_start: 0.7354 (t0) cc_final: 0.6825 (t0) REVERT: A 594 SER cc_start: 0.8652 (p) cc_final: 0.8313 (p) REVERT: A 597 PHE cc_start: 0.7881 (m-80) cc_final: 0.7265 (t80) REVERT: A 664 ARG cc_start: 0.8055 (mmm-85) cc_final: 0.7242 (ttm170) REVERT: A 687 MET cc_start: 0.7457 (ptp) cc_final: 0.7198 (ptp) REVERT: A 704 LEU cc_start: 0.7673 (mt) cc_final: 0.7317 (mt) REVERT: a 60 LYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6594 (tttt) REVERT: a 213 MET cc_start: 0.7219 (mtt) cc_final: 0.6806 (mtm) REVERT: a 218 LEU cc_start: 0.7068 (tp) cc_final: 0.6850 (mm) REVERT: a 242 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7050 (mt-10) REVERT: a 245 MET cc_start: 0.7128 (tpt) cc_final: 0.6768 (tpp) REVERT: a 274 ASP cc_start: 0.7630 (p0) cc_final: 0.6937 (p0) REVERT: a 275 MET cc_start: 0.8100 (tpt) cc_final: 0.6694 (mtm) REVERT: a 296 ILE cc_start: 0.8834 (mt) cc_final: 0.8485 (tt) REVERT: a 315 LYS cc_start: 0.7363 (mmtt) cc_final: 0.6713 (tptm) REVERT: a 377 ILE cc_start: 0.8434 (mt) cc_final: 0.8155 (mt) REVERT: a 401 ASN cc_start: 0.6872 (m-40) cc_final: 0.6520 (t0) REVERT: a 403 MET cc_start: 0.7009 (tpp) cc_final: 0.5037 (tmm) REVERT: a 411 TRP cc_start: 0.7319 (m100) cc_final: 0.6528 (m-90) REVERT: a 424 ILE cc_start: 0.8307 (mt) cc_final: 0.8051 (mt) REVERT: a 482 ASP cc_start: 0.8096 (m-30) cc_final: 0.7537 (m-30) REVERT: a 483 TRP cc_start: 0.8005 (t60) cc_final: 0.7733 (t60) REVERT: a 535 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.7466 (p) REVERT: a 545 TRP cc_start: 0.8696 (m100) cc_final: 0.7611 (m100) REVERT: a 561 TYR cc_start: 0.8431 (t80) cc_final: 0.7916 (t80) REVERT: a 625 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8445 (p90) REVERT: a 645 GLN cc_start: 0.8998 (mt0) cc_final: 0.8526 (mt0) REVERT: a 646 THR cc_start: 0.8832 (m) cc_final: 0.8333 (p) REVERT: a 678 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8531 (m) REVERT: C 34 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7606 (tp) REVERT: C 47 ARG cc_start: 0.7145 (mmt180) cc_final: 0.6835 (mmm160) REVERT: C 64 MET cc_start: 0.6877 (mtm) cc_final: 0.6616 (mtp) REVERT: C 90 MET cc_start: 0.6579 (mtp) cc_final: 0.6220 (mtp) REVERT: c 97 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7291 (tpt-90) REVERT: c 118 GLU cc_start: 0.5476 (tt0) cc_final: 0.5185 (tt0) REVERT: D 88 ILE cc_start: 0.4126 (OUTLIER) cc_final: 0.3892 (pt) REVERT: U 17 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7590 (tt0) REVERT: U 31 LYS cc_start: 0.8384 (mtmt) cc_final: 0.8075 (mtpp) REVERT: U 94 GLU cc_start: 0.6985 (pm20) cc_final: 0.6378 (pm20) REVERT: U 140 MET cc_start: 0.7888 (mmm) cc_final: 0.7083 (mtt) REVERT: U 204 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7681 (mt-10) REVERT: U 208 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7383 (pt) REVERT: U 314 LYS cc_start: 0.8502 (ttpt) cc_final: 0.8255 (ttmt) REVERT: U 357 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7261 (m) REVERT: V 30 VAL cc_start: 0.9004 (t) cc_final: 0.8798 (p) REVERT: V 31 LYS cc_start: 0.8113 (mttt) cc_final: 0.7201 (mttt) REVERT: V 109 PHE cc_start: 0.8568 (t80) cc_final: 0.8355 (t80) REVERT: V 161 ASP cc_start: 0.7536 (t70) cc_final: 0.7055 (t0) REVERT: V 164 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6498 (tm-30) REVERT: V 198 GLN cc_start: 0.8260 (mt0) cc_final: 0.7996 (mm-40) REVERT: V 247 LYS cc_start: 0.7832 (mttt) cc_final: 0.7407 (mttp) REVERT: V 255 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7303 (mm-30) REVERT: V 321 TYR cc_start: 0.8287 (m-10) cc_final: 0.7670 (m-10) REVERT: W 64 PHE cc_start: 0.7360 (m-80) cc_final: 0.6610 (m-80) REVERT: W 66 ARG cc_start: 0.6851 (ttp-170) cc_final: 0.6542 (ttm170) REVERT: W 103 MET cc_start: 0.7172 (ppp) cc_final: 0.6741 (ppp) REVERT: W 104 VAL cc_start: 0.7741 (OUTLIER) cc_final: 0.7534 (t) REVERT: W 180 ILE cc_start: 0.8734 (tp) cc_final: 0.8474 (tp) REVERT: W 268 LYS cc_start: 0.7521 (ttmt) cc_final: 0.7118 (pttp) REVERT: W 292 LEU cc_start: 0.8781 (mp) cc_final: 0.8321 (mt) REVERT: W 314 LYS cc_start: 0.7468 (ttmt) cc_final: 0.6667 (ttpt) REVERT: W 319 LYS cc_start: 0.7418 (tptp) cc_final: 0.7137 (mptt) outliers start: 84 outliers final: 54 residues processed: 665 average time/residue: 0.1688 time to fit residues: 180.8611 Evaluate side-chains 651 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 587 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 225 TRP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 559 CYS Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain a residue 60 LYS Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 158 ILE Chi-restraints excluded: chain a residue 289 ILE Chi-restraints excluded: chain a residue 409 SER Chi-restraints excluded: chain a residue 528 LEU Chi-restraints excluded: chain a residue 535 THR Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 625 PHE Chi-restraints excluded: chain a residue 626 ILE Chi-restraints excluded: chain a residue 661 VAL Chi-restraints excluded: chain a residue 678 THR Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 97 ARG Chi-restraints excluded: chain c residue 101 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 50 ASP Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 127 SER Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain U residue 208 LEU Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain U residue 317 LEU Chi-restraints excluded: chain U residue 357 VAL Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain V residue 191 THR Chi-restraints excluded: chain V residue 293 ILE Chi-restraints excluded: chain W residue 18 ILE Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 136 ASN Chi-restraints excluded: chain W residue 191 THR Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 317 LEU Chi-restraints excluded: chain W residue 332 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 140 optimal weight: 0.0010 chunk 82 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 246 optimal weight: 0.0370 chunk 142 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 overall best weight: 0.5868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** a 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 GLN ** V 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 144 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.186569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.170081 restraints weight = 36597.453| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.03 r_work: 0.3703 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27442 Z= 0.141 Angle : 0.878 41.301 37987 Z= 0.326 Chirality : 0.043 0.175 3792 Planarity : 0.004 0.047 4594 Dihedral : 13.802 176.661 4795 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.30 % Allowed : 24.62 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2767 helix: 1.22 (0.15), residues: 1153 sheet: -0.26 (0.22), residues: 498 loop : -1.12 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 222 TYR 0.037 0.002 TYR A 561 PHE 0.064 0.002 PHE A 301 TRP 0.042 0.002 TRP A 624 HIS 0.010 0.001 HIS U 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (27408) covalent geometry : angle 0.75304 / 0.32 (37951) hydrogen bonds : bond 0.03812 / 2.54 ( 1308) hydrogen bonds : angle 5.03656 / 3.68 ( 3747) metal coordination : bond 0.01004 / 0.62 ( 12) metal coordination : angle 14.65553 / 8.69 ( 36) Misc. bond : bond 0.01439 / 0.69 ( 22) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 605 time to evaluate : 0.673 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 61 TRP cc_start: 0.9227 (p-90) cc_final: 0.8919 (p-90) REVERT: A 90 MET cc_start: 0.9131 (mmm) cc_final: 0.8649 (mmt) REVERT: A 130 SER cc_start: 0.8605 (t) cc_final: 0.8327 (m) REVERT: A 212 TYR cc_start: 0.8685 (t80) cc_final: 0.8368 (t80) REVERT: A 245 MET cc_start: 0.8656 (mmm) cc_final: 0.8197 (tpp) REVERT: A 275 MET cc_start: 0.6983 (mmp) cc_final: 0.6615 (mmt) REVERT: A 303 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7289 (mm-40) REVERT: A 315 LYS cc_start: 0.8415 (tptp) cc_final: 0.7913 (mttm) REVERT: A 344 LYS cc_start: 0.6786 (pttt) cc_final: 0.6099 (mttt) REVERT: A 408 LYS cc_start: 0.7933 (tppp) cc_final: 0.7715 (tppp) REVERT: A 495 PHE cc_start: 0.8198 (t80) cc_final: 0.7969 (t80) REVERT: A 548 MET cc_start: 0.7533 (mtm) cc_final: 0.7264 (mtm) REVERT: A 583 ASP cc_start: 0.7345 (t0) cc_final: 0.6806 (t0) REVERT: A 594 SER cc_start: 0.8678 (p) cc_final: 0.8367 (p) REVERT: A 664 ARG cc_start: 0.8090 (mmm-85) cc_final: 0.7230 (ttm170) REVERT: A 687 MET cc_start: 0.7461 (ptp) cc_final: 0.7191 (ptp) REVERT: A 704 LEU cc_start: 0.7673 (mt) cc_final: 0.7314 (mt) REVERT: a 82 LEU cc_start: 0.8408 (mt) cc_final: 0.8016 (mt) REVERT: a 99 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7400 (tp-100) REVERT: a 146 TRP cc_start: 0.7441 (m100) cc_final: 0.6808 (m100) REVERT: a 213 MET cc_start: 0.7163 (mtt) cc_final: 0.6746 (mtm) REVERT: a 245 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6660 (tpp) REVERT: a 274 ASP cc_start: 0.7641 (p0) cc_final: 0.6855 (p0) REVERT: a 275 MET cc_start: 0.8265 (tpt) cc_final: 0.6735 (mtm) REVERT: a 296 ILE cc_start: 0.8829 (mt) cc_final: 0.8484 (tt) REVERT: a 315 LYS cc_start: 0.7548 (mmtt) cc_final: 0.6949 (tptm) REVERT: a 357 LYS cc_start: 0.7503 (mtmt) cc_final: 0.7270 (tttt) REVERT: a 377 ILE cc_start: 0.8458 (mt) cc_final: 0.8172 (mt) REVERT: a 378 ILE cc_start: 0.8872 (tt) cc_final: 0.8642 (tt) REVERT: a 401 ASN cc_start: 0.6870 (m-40) cc_final: 0.6532 (t0) REVERT: a 403 MET cc_start: 0.7051 (tpp) cc_final: 0.5112 (tmm) REVERT: a 411 TRP cc_start: 0.7317 (m100) cc_final: 0.6525 (m-90) REVERT: a 424 ILE cc_start: 0.8306 (mt) cc_final: 0.8042 (mt) REVERT: a 482 ASP cc_start: 0.8117 (m-30) cc_final: 0.7646 (m-30) REVERT: a 483 TRP cc_start: 0.8019 (t60) cc_final: 0.7743 (t60) REVERT: a 535 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7474 (p) REVERT: a 545 TRP cc_start: 0.8669 (m100) cc_final: 0.7754 (m100) REVERT: a 561 TYR cc_start: 0.8421 (t80) cc_final: 0.8068 (t80) REVERT: a 645 GLN cc_start: 0.9040 (mt0) cc_final: 0.8551 (mt0) REVERT: a 646 THR cc_start: 0.8835 (m) cc_final: 0.8347 (p) REVERT: C 34 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7621 (tp) REVERT: C 47 ARG cc_start: 0.7154 (mmt180) cc_final: 0.6849 (mmm160) REVERT: C 64 MET cc_start: 0.6910 (mtm) cc_final: 0.6652 (mtp) REVERT: C 90 MET cc_start: 0.6483 (mtp) cc_final: 0.6140 (mtp) REVERT: c 118 GLU cc_start: 0.5525 (tt0) cc_final: 0.5232 (tt0) REVERT: D 88 ILE cc_start: 0.4051 (OUTLIER) cc_final: 0.3845 (pt) REVERT: U 17 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7471 (tt0) REVERT: U 31 LYS cc_start: 0.8397 (mtmt) cc_final: 0.8097 (mtpp) REVERT: U 94 GLU cc_start: 0.6987 (pm20) cc_final: 0.6378 (pm20) REVERT: U 103 MET cc_start: 0.7864 (tmm) cc_final: 0.7528 (ppp) REVERT: U 140 MET cc_start: 0.7840 (mmm) cc_final: 0.7079 (mtt) REVERT: U 208 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7343 (pt) REVERT: U 268 LYS cc_start: 0.8344 (pttm) cc_final: 0.7254 (pptt) REVERT: U 314 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8071 (pttt) REVERT: U 325 TYR cc_start: 0.8047 (t80) cc_final: 0.7703 (t80) REVERT: U 357 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7279 (m) REVERT: V 31 LYS cc_start: 0.8121 (mttt) cc_final: 0.7275 (mtmt) REVERT: V 161 ASP cc_start: 0.7573 (t70) cc_final: 0.7082 (t0) REVERT: V 164 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6516 (tm-30) REVERT: V 198 GLN cc_start: 0.8243 (mt0) cc_final: 0.7947 (mm-40) REVERT: V 224 ARG cc_start: 0.8155 (mtm110) cc_final: 0.7912 (mtm110) REVERT: V 247 LYS cc_start: 0.7830 (mttt) cc_final: 0.7410 (mttp) REVERT: V 255 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7185 (mm-30) REVERT: V 321 TYR cc_start: 0.8298 (m-10) cc_final: 0.7691 (m-10) REVERT: W 64 PHE cc_start: 0.7329 (m-80) cc_final: 0.6620 (m-80) REVERT: W 66 ARG cc_start: 0.6883 (ttp-170) cc_final: 0.6586 (ttm170) REVERT: W 103 MET cc_start: 0.7202 (ppp) cc_final: 0.6788 (ppp) REVERT: W 104 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7521 (t) REVERT: W 180 ILE cc_start: 0.8746 (tp) cc_final: 0.8491 (tp) REVERT: W 222 ARG cc_start: 0.6514 (ttm110) cc_final: 0.6301 (ttm110) REVERT: W 268 LYS cc_start: 0.7516 (ttmt) cc_final: 0.7158 (pttp) REVERT: W 292 LEU cc_start: 0.8791 (mp) cc_final: 0.8279 (mt) REVERT: W 319 LYS cc_start: 0.7412 (tptp) cc_final: 0.7131 (mptt) outliers start: 77 outliers final: 59 residues processed: 646 average time/residue: 0.1631 time to fit residues: 169.2950 Evaluate side-chains 655 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 589 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 225 TRP Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 559 CYS Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 158 ILE Chi-restraints excluded: chain a residue 245 MET Chi-restraints excluded: chain a residue 289 ILE Chi-restraints excluded: chain a residue 381 VAL Chi-restraints excluded: chain a residue 409 SER Chi-restraints excluded: chain a residue 528 LEU Chi-restraints excluded: chain a residue 535 THR Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 626 ILE Chi-restraints excluded: chain a residue 661 VAL Chi-restraints excluded: chain a residue 682 PHE Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 97 ARG Chi-restraints excluded: chain c residue 101 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 50 ASP Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 127 SER Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain U residue 208 LEU Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain U residue 246 ASP Chi-restraints excluded: chain U residue 293 ILE Chi-restraints excluded: chain U residue 317 LEU Chi-restraints excluded: chain U residue 357 VAL Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 293 ILE Chi-restraints excluded: chain W residue 18 ILE Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 136 ASN Chi-restraints excluded: chain W residue 191 THR Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 203 ILE Chi-restraints excluded: chain W residue 317 LEU Chi-restraints excluded: chain W residue 332 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 39 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 259 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 303 GLN ** a 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 699 GLN ** U 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 144 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.183728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.167201 restraints weight = 36468.130| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.01 r_work: 0.3705 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27442 Z= 0.168 Angle : 0.894 39.383 37987 Z= 0.334 Chirality : 0.044 0.214 3792 Planarity : 0.005 0.050 4594 Dihedral : 13.739 176.394 4795 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.35 % Allowed : 24.71 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.16), residues: 2767 helix: 1.21 (0.15), residues: 1143 sheet: -0.31 (0.22), residues: 500 loop : -1.08 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 104 TYR 0.043 0.002 TYR A 561 PHE 0.062 0.002 PHE A 301 TRP 0.042 0.002 TRP A 624 HIS 0.011 0.001 HIS U 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (27408) covalent geometry : angle 0.77086 / 0.33 (37951) hydrogen bonds : bond 0.03890 / 2.59 ( 1308) hydrogen bonds : angle 5.09187 / 3.71 ( 3747) metal coordination : bond 0.01257 / 0.76 ( 12) metal coordination : angle 14.74181 / 8.67 ( 36) Misc. bond : bond 0.01731 / 0.69 ( 22) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5534 Ramachandran restraints generated. 2767 Oldfield, 0 Emsley, 2767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 590 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TRP cc_start: 0.9247 (p-90) cc_final: 0.8965 (p-90) REVERT: A 90 MET cc_start: 0.9125 (mmm) cc_final: 0.8663 (mmt) REVERT: A 130 SER cc_start: 0.8576 (t) cc_final: 0.8350 (m) REVERT: A 168 ASN cc_start: 0.8612 (t0) cc_final: 0.8333 (t0) REVERT: A 245 MET cc_start: 0.8664 (mmm) cc_final: 0.8196 (tpp) REVERT: A 275 MET cc_start: 0.7037 (mmp) cc_final: 0.6693 (mmt) REVERT: A 303 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7307 (mm-40) REVERT: A 315 LYS cc_start: 0.8484 (tptp) cc_final: 0.7998 (mttm) REVERT: A 344 LYS cc_start: 0.6802 (pttt) cc_final: 0.6150 (mttt) REVERT: A 495 PHE cc_start: 0.8276 (t80) cc_final: 0.8033 (t80) REVERT: A 548 MET cc_start: 0.7554 (mtm) cc_final: 0.7301 (mtm) REVERT: A 583 ASP cc_start: 0.7353 (t0) cc_final: 0.6852 (t0) REVERT: A 594 SER cc_start: 0.8727 (p) cc_final: 0.8399 (p) REVERT: A 664 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7261 (ttm170) REVERT: A 679 PHE cc_start: 0.8156 (m-10) cc_final: 0.7878 (m-80) REVERT: A 687 MET cc_start: 0.7600 (ptp) cc_final: 0.7326 (ptp) REVERT: a 82 LEU cc_start: 0.8452 (mt) cc_final: 0.8067 (mt) REVERT: a 99 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7502 (tp-100) REVERT: a 213 MET cc_start: 0.7129 (mtt) cc_final: 0.6711 (mtm) REVERT: a 245 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6801 (tpp) REVERT: a 274 ASP cc_start: 0.7701 (p0) cc_final: 0.6828 (p0) REVERT: a 275 MET cc_start: 0.8202 (tpt) cc_final: 0.6766 (mtm) REVERT: a 296 ILE cc_start: 0.8867 (mt) cc_final: 0.8527 (tt) REVERT: a 315 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7260 (tptm) REVERT: a 318 PHE cc_start: 0.6876 (m-80) cc_final: 0.6663 (m-80) REVERT: a 357 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7356 (tttt) REVERT: a 377 ILE cc_start: 0.8542 (mt) cc_final: 0.8278 (mt) REVERT: a 401 ASN cc_start: 0.6897 (m-40) cc_final: 0.6521 (t0) REVERT: a 403 MET cc_start: 0.7151 (tpp) cc_final: 0.5218 (tmm) REVERT: a 424 ILE cc_start: 0.8296 (mt) cc_final: 0.8036 (mt) REVERT: a 482 ASP cc_start: 0.8208 (m-30) cc_final: 0.7710 (m-30) REVERT: a 483 TRP cc_start: 0.8052 (t60) cc_final: 0.7768 (t60) REVERT: a 545 TRP cc_start: 0.8672 (m100) cc_final: 0.8060 (m100) REVERT: a 548 MET cc_start: 0.8156 (mtp) cc_final: 0.7663 (mtt) REVERT: a 561 TYR cc_start: 0.8441 (t80) cc_final: 0.8070 (t80) REVERT: a 645 GLN cc_start: 0.9085 (mt0) cc_final: 0.8542 (mt0) REVERT: a 646 THR cc_start: 0.8749 (m) cc_final: 0.8276 (p) REVERT: C 34 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7639 (tp) REVERT: C 47 ARG cc_start: 0.7175 (mmt180) cc_final: 0.6874 (mmm160) REVERT: C 64 MET cc_start: 0.6970 (mtm) cc_final: 0.6678 (mtp) REVERT: C 90 MET cc_start: 0.6223 (mtp) cc_final: 0.5739 (mtp) REVERT: c 118 GLU cc_start: 0.5472 (tt0) cc_final: 0.5181 (tt0) REVERT: D 88 ILE cc_start: 0.4107 (OUTLIER) cc_final: 0.3892 (pt) REVERT: U 31 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8095 (mtpp) REVERT: U 85 GLU cc_start: 0.7475 (mt-10) cc_final: 0.6753 (mp0) REVERT: U 94 GLU cc_start: 0.6969 (pm20) cc_final: 0.6394 (pm20) REVERT: U 103 MET cc_start: 0.7846 (tmm) cc_final: 0.7563 (ppp) REVERT: U 140 MET cc_start: 0.7898 (mmm) cc_final: 0.7315 (mtt) REVERT: U 208 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7402 (pt) REVERT: U 268 LYS cc_start: 0.8475 (pttm) cc_final: 0.7372 (pptt) REVERT: U 325 TYR cc_start: 0.8079 (t80) cc_final: 0.7816 (t80) REVERT: V 31 LYS cc_start: 0.8111 (mttt) cc_final: 0.7230 (mttt) REVERT: V 161 ASP cc_start: 0.7579 (t70) cc_final: 0.7126 (t0) REVERT: V 164 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6555 (tm-30) REVERT: V 224 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7814 (mtm110) REVERT: V 247 LYS cc_start: 0.7832 (mttt) cc_final: 0.7447 (mttp) REVERT: V 255 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7113 (mm-30) REVERT: V 295 LEU cc_start: 0.8750 (mt) cc_final: 0.8481 (mt) REVERT: V 321 TYR cc_start: 0.8249 (m-10) cc_final: 0.7659 (m-10) REVERT: W 64 PHE cc_start: 0.7184 (m-80) cc_final: 0.6596 (m-80) REVERT: W 66 ARG cc_start: 0.6926 (ttp-170) cc_final: 0.6630 (ttm170) REVERT: W 103 MET cc_start: 0.7244 (ppp) cc_final: 0.6845 (ppp) REVERT: W 104 VAL cc_start: 0.7802 (OUTLIER) cc_final: 0.7594 (t) REVERT: W 180 ILE cc_start: 0.8730 (tp) cc_final: 0.8470 (tp) REVERT: W 268 LYS cc_start: 0.7533 (ttmt) cc_final: 0.7256 (pttp) REVERT: W 292 LEU cc_start: 0.8775 (mp) cc_final: 0.8319 (mt) REVERT: W 319 LYS cc_start: 0.7416 (tptp) cc_final: 0.7091 (mptt) REVERT: W 361 GLU cc_start: 0.7460 (tt0) cc_final: 0.7196 (tt0) outliers start: 78 outliers final: 63 residues processed: 633 average time/residue: 0.1574 time to fit residues: 161.2539 Evaluate side-chains 656 residues out of total 2331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 588 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 225 TRP Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 631 TRP Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 116 THR Chi-restraints excluded: chain a residue 137 GLU Chi-restraints excluded: chain a residue 158 ILE Chi-restraints excluded: chain a residue 245 MET Chi-restraints excluded: chain a residue 289 ILE Chi-restraints excluded: chain a residue 381 VAL Chi-restraints excluded: chain a residue 409 SER Chi-restraints excluded: chain a residue 528 LEU Chi-restraints excluded: chain a residue 535 THR Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 626 ILE Chi-restraints excluded: chain a residue 661 VAL Chi-restraints excluded: chain a residue 682 PHE Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 97 ARG Chi-restraints excluded: chain c residue 101 GLU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 50 ASP Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 127 SER Chi-restraints excluded: chain U residue 150 MET Chi-restraints excluded: chain U residue 158 ASP Chi-restraints excluded: chain U residue 208 LEU Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain U residue 246 ASP Chi-restraints excluded: chain U residue 293 ILE Chi-restraints excluded: chain U residue 317 LEU Chi-restraints excluded: chain U residue 323 ILE Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 293 ILE Chi-restraints excluded: chain W residue 18 ILE Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 104 VAL Chi-restraints excluded: chain W residue 108 ASP Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 136 ASN Chi-restraints excluded: chain W residue 191 THR Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 201 SER Chi-restraints excluded: chain W residue 203 ILE Chi-restraints excluded: chain W residue 208 LEU Chi-restraints excluded: chain W residue 317 LEU Chi-restraints excluded: chain W residue 332 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 147 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 206 optimal weight: 0.2980 chunk 165 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 274 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 406 GLN ** a 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.183147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.166674 restraints weight = 36510.460| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.01 r_work: 0.3718 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27442 Z= 0.170 Angle : 0.899 38.706 37987 Z= 0.337 Chirality : 0.044 0.200 3792 Planarity : 0.005 0.054 4594 Dihedral : 13.668 176.408 4795 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.35 % Allowed : 24.97 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.16), residues: 2767 helix: 1.19 (0.15), residues: 1144 sheet: -0.36 (0.22), residues: 500 loop : -1.08 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 131 TYR 0.041 0.002 TYR A 561 PHE 0.061 0.002 PHE A 301 TRP 0.041 0.002 TRP A 624 HIS 0.010 0.001 HIS W 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (27408) covalent geometry : angle 0.77636 / 0.33 (37951) hydrogen bonds : bond 0.03899 / 2.60 ( 1308) hydrogen bonds : angle 5.10116 / 3.72 ( 3747) metal coordination : bond 0.01246 / 0.76 ( 12) metal coordination : angle 14.74424 / 8.63 ( 36) Misc. bond : bond 0.01839 / 0.72 ( 22) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6094.18 seconds wall clock time: 105 minutes 52.16 seconds (6352.16 seconds total)