Starting phenix.real_space_refine on Mon Jul 6 19:35:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ueb_26471/07_2026/7ueb_26471.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ueb_26471/07_2026/7ueb_26471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ueb_26471/07_2026/7ueb_26471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ueb_26471/07_2026/7ueb_26471.map" model { file = "/net/cci-nas-00/data/ceres_data/7ueb_26471/07_2026/7ueb_26471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ueb_26471/07_2026/7ueb_26471.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ueb_26471/07_2026/7ueb_26471.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ueb_26471/07_2026/7ueb_26471.cif" } resolution = 3.08 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= 0.112 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 10 5.49 5 Mg 79 5.21 5 S 138 5.16 5 C 25384 2.51 5 N 5671 2.21 5 O 6274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 148 residue(s): 0.26s 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: 37570 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 5197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5197 Classifications: {'peptide': 650} Link IDs: {'PTRANS': 26, 'TRANS': 623} Chain: "a" Number of atoms: 5214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5214 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 26, 'TRANS': 625} Chain: "B" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 887 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 9, 'TRANS': 104} Chain breaks: 1 Chain: "C" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} 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: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 823 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "E" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 441 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "F" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 379 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "U" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2826 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 343} 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: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2789 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 338} Chain: "X" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2782 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 337} Chain: "Y" 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: "Z" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2789 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 338} Chain: "A" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 1433 Unusual residues: {' CA': 1, 'BCL': 12, 'F26': 1, 'F39': 1, 'G2O': 3, 'GS0': 1, 'LHG': 3, 'LMG': 4, 'SF4': 1} Classifications: {'undetermined': 27} Link IDs: {None: 26} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 1249 Unusual residues: {' CA': 1, 'BCL': 12, 'F26': 2, 'F39': 1, 'G2O': 1, 'GS0': 1, 'LHG': 4, 'LMG': 1} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 67 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: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {'BCL': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'F39': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "E" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "U" 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 Chain: "V" 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: "W" 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: "X" Number of atoms: 554 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 9, 554 Unusual residues: {'BCL': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "Y" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 528 Unusual residues: {'BCL': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "Z" Number of atoms: 485 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 8, 485 Unusual residues: {'BCL': 7, 'LHG': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 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 3742 SG CYS A 527 67.119 104.354 74.652 1.00 46.48 S ATOM 9015 SG CYS a 536 67.610 107.079 68.959 1.00 15.06 S ATOM 3801 SG CYS A 536 62.329 103.396 70.700 1.00 35.14 S ATOM 8956 SG CYS a 527 67.761 100.851 69.022 1.00 38.66 S ATOM 10625 SG CYS B 143 71.019 99.673 79.983 1.00 25.64 S ATOM 10608 SG CYS B 140 73.645 94.102 79.150 1.00 22.86 S ATOM 10846 SG CYS B 172 75.963 96.701 79.135 1.00 38.88 S ATOM 10980 SG CYS B 191 72.210 96.316 84.993 1.00 19.98 S ATOM 10643 SG CYS B 146 77.182 99.094 81.970 1.00 23.84 S ATOM 10846 SG CYS B 172 75.963 96.701 79.135 1.00 38.88 S ATOM 10919 SG CYS B 182 84.769 103.846 88.180 1.00 59.77 S ATOM 10674 SG CYS B 150 84.290 101.643 82.605 1.00 55.04 S ATOM 10936 SG CYS B 185 80.383 99.225 87.254 1.00 53.40 S ATOM 10899 SG CYS B 179 86.274 97.367 87.318 1.00 55.37 S Time building chain proxies: 8.08, per 1000 atoms: 0.22 Number of scatterers: 37570 At special positions: 0 Unit cell: (115.44, 175.76, 187.2, 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 138 16.00 P 10 15.00 Mg 79 11.99 O 6274 8.00 N 5671 7.00 C 25384 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=41, symmetry=0 Number of additional bonds: simple=41, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 824 " pdb="FE2 SF4 A 824 " - pdb=" SG CYS a 536 " pdb="FE4 SF4 A 824 " - pdb=" SG CYS a 527 " pdb="FE1 SF4 A 824 " - pdb=" SG CYS A 527 " pdb="FE3 SF4 A 824 " - pdb=" SG CYS A 536 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 140 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 143 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 146 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 191 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 172 " pdb=" SF4 B 303 " pdb="FE1 SF4 B 303 " - pdb=" SG CYS B 182 " pdb="FE3 SF4 B 303 " - pdb=" SG CYS B 185 " pdb="FE2 SF4 B 303 " - pdb=" SG CYS B 150 " pdb="FE4 SF4 B 303 " - pdb=" SG CYS B 179 " Number of angles added : 39 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7250 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 18 sheets defined 40.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.569A pdb=" N ILE A 64 " --> pdb=" O TRP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 97 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 117 through 124 Processing helix chain 'A' and resid 132 through 167 removed outlier: 3.612A pdb=" N LEU A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.914A pdb=" N ASP A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 227 removed outlier: 4.384A 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: 4.282A pdb=" N GLU A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 302 removed outlier: 3.503A pdb=" N GLN A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) 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 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 401 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 417 through 451 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.991A pdb=" N GLY A 455 " --> pdb=" O ASN A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 removed outlier: 6.080A pdb=" N PHE A 462 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR A 463 " --> pdb=" O MET A 460 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TRP A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.630A pdb=" N GLN A 472 " --> pdb=" O PRO A 469 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP A 473 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET A 474 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 506 removed outlier: 3.652A 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 563 removed outlier: 4.522A pdb=" N LYS A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY A 554 " --> pdb=" O TRP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 596 through 608 removed outlier: 4.257A pdb=" N PHE A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR A 606 " --> pdb=" O THR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 627 removed outlier: 3.539A pdb=" N SER A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 634 through 657 Processing helix chain 'A' and resid 669 through 695 removed outlier: 3.683A pdb=" N LEU A 691 " --> pdb=" O MET A 687 " (cutoff:3.500A) Processing helix chain 'a' and resid 60 through 64 removed outlier: 3.931A 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 95 Processing helix chain 'a' and resid 111 through 124 Proline residue: a 119 - end of helix Processing helix chain 'a' and resid 132 through 166 Processing helix chain 'a' and resid 189 through 194 Processing helix chain 'a' and resid 201 through 227 removed outlier: 4.454A 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 239 through 263 removed outlier: 3.802A pdb=" N THR a 243 " --> pdb=" O ILE a 239 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR a 259 " --> pdb=" O ALA a 255 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP a 260 " --> pdb=" O LEU a 256 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 273 removed outlier: 4.242A pdb=" N LEU a 271 " --> pdb=" O ALA a 267 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN a 272 " --> pdb=" O ALA a 268 " (cutoff:3.500A) removed outlier: 3.625A 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 276 through 302 removed outlier: 3.892A pdb=" N GLN a 302 " --> pdb=" O PHE a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 306 through 311 Processing helix chain 'a' and resid 312 through 315 Processing helix chain 'a' and resid 359 through 363 Processing helix chain 'a' and resid 363 through 401 Processing helix chain 'a' and resid 409 through 414 Processing helix chain 'a' and resid 419 through 452 removed outlier: 3.966A pdb=" N LEU a 425 " --> pdb=" O GLN a 421 " (cutoff:3.500A) Processing helix chain 'a' and resid 453 through 456 Processing helix chain 'a' and resid 457 through 461 Processing helix chain 'a' and resid 479 through 505 removed outlier: 3.689A 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: 4.363A pdb=" N LYS a 553 " --> pdb=" O LEU a 549 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY a 554 " --> pdb=" O TRP a 550 " (cutoff:3.500A) Processing helix chain 'a' and resid 578 through 580 No H-bonds generated for 'chain 'a' and resid 578 through 580' Processing helix chain 'a' and resid 581 through 586 Processing helix chain 'a' and resid 595 through 609 removed outlier: 3.813A pdb=" N PHE a 600 " --> pdb=" O ILE a 596 " (cutoff:3.500A) removed outlier: 4.132A 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) removed outlier: 3.718A pdb=" N ILE a 607 " --> pdb=" O GLU a 603 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER a 609 " --> pdb=" O VAL a 605 " (cutoff:3.500A) Processing helix chain 'a' and resid 610 through 627 Processing helix chain 'a' and resid 627 through 632 Processing helix chain 'a' and resid 634 through 656 removed outlier: 3.519A pdb=" N ILE a 644 " --> pdb=" O GLU a 640 " (cutoff:3.500A) Processing helix chain 'a' and resid 669 through 687 Processing helix chain 'a' and resid 688 through 696 removed outlier: 4.132A pdb=" N GLY a 696 " --> pdb=" O PHE a 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.557A pdb=" N GLY B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 43 through 73 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 79 through 99 removed outlier: 3.539A pdb=" N LEU C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.634A pdb=" N ASN C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 23 through 30 Processing helix chain 'c' and resid 42 through 73 Processing helix chain 'c' and resid 79 through 99 Processing helix chain 'c' and resid 115 through 125 Processing helix chain 'D' and resid 63 through 72 Processing helix chain 'E' and resid 17 through 24 Processing helix chain 'E' and resid 35 through 54 Proline residue: E 50 - end of helix Processing helix chain 'F' and resid 4 through 12 Processing helix chain 'F' and resid 12 through 18 Processing helix chain 'F' and resid 21 through 34 Processing helix chain 'F' and resid 37 through 52 Processing helix chain 'U' and resid 127 through 134 removed outlier: 4.049A pdb=" N ARG U 131 " --> pdb=" O SER U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 173 removed outlier: 3.640A pdb=" N GLY U 171 " --> pdb=" O VAL U 167 " (cutoff:3.500A) Processing helix chain 'U' and resid 175 through 185 removed outlier: 4.547A pdb=" N ARG U 181 " --> pdb=" O ASN U 177 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP U 182 " --> pdb=" O ASP U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 188 through 196 removed outlier: 3.741A 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 291 through 300 removed outlier: 4.117A pdb=" N LEU U 295 " --> pdb=" O PRO U 291 " (cutoff:3.500A) Processing helix chain 'U' and resid 343 through 353 Processing helix chain 'V' and resid 127 through 134 removed outlier: 3.728A 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: 5.023A pdb=" N ARG V 181 " --> pdb=" O ASN V 177 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP V 182 " --> pdb=" O ASP V 178 " (cutoff:3.500A) Processing helix chain 'V' and resid 188 through 194 removed outlier: 3.862A 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 291 through 303 removed outlier: 4.142A pdb=" N LEU V 295 " --> pdb=" O PRO V 291 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET V 300 " --> pdb=" O VAL V 296 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL V 301 " --> pdb=" O HIS V 297 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS V 303 " --> pdb=" O GLY V 299 " (cutoff:3.500A) Processing helix chain 'V' and resid 343 through 354 Processing helix chain 'W' and resid 127 through 134 removed outlier: 3.828A pdb=" N ARG W 131 " --> pdb=" O SER W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 156 through 173 Processing helix chain 'W' and resid 175 through 185 removed outlier: 4.424A pdb=" N ARG W 181 " --> pdb=" O ASN W 177 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASP W 182 " --> pdb=" O ASP W 178 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE W 183 " --> pdb=" O TRP W 179 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 196 removed outlier: 3.862A pdb=" N ASN W 194 " --> pdb=" O PHE W 190 " (cutoff:3.500A) Processing helix chain 'W' and resid 233 through 238 Processing helix chain 'W' and resid 238 through 243 removed outlier: 3.849A pdb=" N PHE W 243 " --> pdb=" O TRP W 239 " (cutoff:3.500A) Processing helix chain 'W' and resid 291 through 303 removed outlier: 4.200A pdb=" N LEU W 295 " --> pdb=" O PRO W 291 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL W 301 " --> pdb=" O HIS W 297 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS W 303 " --> pdb=" O GLY W 299 " (cutoff:3.500A) Processing helix chain 'W' and resid 342 through 354 Processing helix chain 'X' and resid 127 through 134 removed outlier: 3.791A pdb=" N ARG X 131 " --> pdb=" O SER X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 173 Processing helix chain 'X' and resid 175 through 185 removed outlier: 4.493A pdb=" N ARG X 181 " --> pdb=" O ASN X 177 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP X 182 " --> pdb=" O ASP X 178 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE X 183 " --> pdb=" O TRP X 179 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 196 removed outlier: 3.620A pdb=" N ASN X 194 " --> pdb=" O PHE X 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 238 Processing helix chain 'X' and resid 291 through 303 removed outlier: 4.334A pdb=" N LEU X 295 " --> pdb=" O PRO X 291 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET X 300 " --> pdb=" O VAL X 296 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL X 301 " --> pdb=" O HIS X 297 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS X 303 " --> pdb=" O GLY X 299 " (cutoff:3.500A) Processing helix chain 'X' and resid 343 through 354 Processing helix chain 'Y' and resid 127 through 134 removed outlier: 3.574A pdb=" N ARG Y 131 " --> pdb=" O SER Y 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 156 through 171 Processing helix chain 'Y' and resid 175 through 185 removed outlier: 4.898A pdb=" N ARG Y 181 " --> pdb=" O ASN Y 177 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP Y 182 " --> pdb=" O ASP Y 178 " (cutoff:3.500A) Processing helix chain 'Y' and resid 188 through 196 removed outlier: 3.840A pdb=" N ASN Y 194 " --> pdb=" O PHE Y 190 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY Y 196 " --> pdb=" O ALA Y 192 " (cutoff:3.500A) Processing helix chain 'Y' and resid 233 through 238 Processing helix chain 'Y' and resid 238 through 243 removed outlier: 4.129A pdb=" N PHE Y 243 " --> pdb=" O TRP Y 239 " (cutoff:3.500A) Processing helix chain 'Y' and resid 291 through 303 removed outlier: 4.213A pdb=" N LEU Y 295 " --> pdb=" O PRO Y 291 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET Y 300 " --> pdb=" O VAL Y 296 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL Y 301 " --> pdb=" O HIS Y 297 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 354 Processing helix chain 'Z' and resid 60 through 63 Processing helix chain 'Z' and resid 127 through 132 removed outlier: 3.681A pdb=" N ARG Z 131 " --> pdb=" O SER Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 156 through 171 removed outlier: 3.538A pdb=" N ILE Z 160 " --> pdb=" O ASN Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 175 through 184 removed outlier: 4.520A pdb=" N ARG Z 181 " --> pdb=" O ASN Z 177 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP Z 182 " --> pdb=" O ASP Z 178 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 196 removed outlier: 3.793A pdb=" N ASN Z 194 " --> pdb=" O PHE Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 233 through 238 Processing helix chain 'Z' and resid 238 through 243 removed outlier: 3.888A pdb=" N PHE Z 243 " --> pdb=" O TRP Z 239 " (cutoff:3.500A) Processing helix chain 'Z' and resid 291 through 303 removed outlier: 4.272A pdb=" N LEU Z 295 " --> pdb=" O PRO Z 291 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET Z 300 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL Z 301 " --> pdb=" O HIS Z 297 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS Z 303 " --> pdb=" O GLY Z 299 " (cutoff:3.500A) Processing helix chain 'Z' and resid 343 through 354 Processing sheet with id=AA1, first strand: chain 'A' and resid 565 through 566 removed outlier: 3.537A pdb=" N TRP A 566 " --> pdb=" O SER A 594 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'a' and resid 317 through 318 removed outlier: 3.816A pdb=" N LYS a 357 " --> pdb=" O PHE a 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 135 Processing sheet with id=AA4, first strand: chain 'B' and resid 157 through 160 Processing sheet with id=AA5, first strand: chain 'D' and resid 50 through 53 removed outlier: 3.867A pdb=" N SER D 38 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL D 52 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE D 36 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 110 " --> pdb=" O ILE D 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'U' and resid 10 through 20 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 28 through 36 current: chain 'U' and resid 65 through 75 removed outlier: 5.541A pdb=" N THR U 112 " --> pdb=" O PRO U 153 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU U 116 " --> pdb=" O LEU U 149 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU U 149 " --> pdb=" O GLU U 116 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 142 through 153 current: chain 'U' and resid 216 through 229 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 216 through 229 current: chain 'U' and resid 265 through 273 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 265 through 273 current: chain 'U' and resid 337 through 341 Processing sheet with id=AA7, first strand: chain 'U' and resid 277 through 281 removed outlier: 6.734A pdb=" N LEU U 284 " --> pdb=" O ALA U 280 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE U 362 " --> pdb=" O ILE U 287 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU U 361 " --> pdb=" O ALA U 327 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA U 327 " --> pdb=" O GLU U 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 11 through 20 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 28 through 36 current: chain 'V' and resid 64 through 75 removed outlier: 4.449A pdb=" N VAL V 99 " --> pdb=" O ASP V 87 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG V 95 " --> pdb=" O GLU V 91 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR V 112 " --> pdb=" O PRO V 153 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU V 149 " --> pdb=" O GLU V 116 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 142 through 153 current: chain 'V' and resid 217 through 229 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 217 through 229 current: chain 'V' and resid 264 through 273 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 264 through 273 current: chain 'V' and resid 337 through 341 Processing sheet with id=AA9, first strand: chain 'V' and resid 277 through 279 removed outlier: 5.237A pdb=" N ILE V 362 " --> pdb=" O ILE V 287 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU V 361 " --> pdb=" O ALA V 326 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA V 326 " --> pdb=" O GLU V 361 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU V 363 " --> pdb=" O ARG V 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 11 through 14 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 11 through 14 current: chain 'W' and resid 28 through 36 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 28 through 36 current: chain 'W' and resid 64 through 75 removed outlier: 4.101A pdb=" N LEU W 82 " --> pdb=" O PHE W 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 142 through 151 current: chain 'W' and resid 221 through 229 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 221 through 229 current: chain 'W' and resid 268 through 273 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 268 through 273 current: chain 'W' and resid 337 through 340 Processing sheet with id=AB2, first strand: chain 'W' and resid 277 through 278 Processing sheet with id=AB3, first strand: chain 'W' and resid 323 through 327 removed outlier: 6.959A pdb=" N LEU W 363 " --> pdb=" O ARG W 324 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA W 326 " --> pdb=" O GLU W 361 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU W 361 " --> pdb=" O ALA W 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'X' and resid 11 through 20 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 28 through 36 current: chain 'X' and resid 64 through 70 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 64 through 70 current: chain 'X' and resid 78 through 89 removed outlier: 5.411A pdb=" N THR X 112 " --> pdb=" O PRO X 153 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 142 through 153 current: chain 'X' and resid 217 through 229 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 217 through 229 current: chain 'X' and resid 265 through 273 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 265 through 273 current: chain 'X' and resid 337 through 341 Processing sheet with id=AB5, first strand: chain 'X' and resid 277 through 279 removed outlier: 4.959A pdb=" N ILE X 362 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU X 361 " --> pdb=" O ALA X 326 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA X 326 " --> pdb=" O GLU X 361 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 10 through 20 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 28 through 36 current: chain 'Y' and resid 64 through 75 removed outlier: 5.481A pdb=" N THR Y 112 " --> pdb=" O PRO Y 153 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER Y 118 " --> pdb=" O ASP Y 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 142 through 153 current: chain 'Y' and resid 216 through 229 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 216 through 229 current: chain 'Y' and resid 265 through 273 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 265 through 273 current: chain 'Y' and resid 337 through 340 Processing sheet with id=AB7, first strand: chain 'Y' and resid 277 through 279 removed outlier: 6.868A pdb=" N LEU Y 363 " --> pdb=" O ARG Y 324 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Z' and resid 11 through 20 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 28 through 36 current: chain 'Z' and resid 64 through 75 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 109 through 115 current: chain 'Z' and resid 141 through 153 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 141 through 153 current: chain 'Z' and resid 218 through 230 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 218 through 230 current: chain 'Z' and resid 264 through 273 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 264 through 273 current: chain 'Z' and resid 337 through 341 Processing sheet with id=AB9, first strand: chain 'Z' and resid 277 through 281 removed outlier: 6.750A pdb=" N LEU Z 284 " --> pdb=" O ALA Z 280 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE Z 362 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU Z 363 " --> pdb=" O ARG Z 324 " (cutoff:3.500A) 1365 hydrogen bonds defined for protein. 3972 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: 7.69 Time building geometry restraints manager: 4.98 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: 10835 1.36 - 1.62: 27677 1.62 - 1.87: 226 1.87 - 2.13: 227 2.13 - 2.39: 125 Bond restraints: 39090 Sorted by residual: bond pdb=" ND G2O A 826 " pdb="MG G2O A 826 " ideal model delta sigma weight residual 2.005 2.393 -0.388 2.00e-02 2.50e+03 3.76e+02 bond pdb=" ND G2O a 801 " pdb="MG G2O a 801 " ideal model delta sigma weight residual 2.005 2.360 -0.355 2.00e-02 2.50e+03 3.15e+02 bond pdb=" ND G2O A 827 " pdb="MG G2O A 827 " 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 802 " pdb="MG G2O A 802 " ideal model delta sigma weight residual 2.005 2.336 -0.331 2.00e-02 2.50e+03 2.74e+02 bond pdb=" NC G2O a 801 " pdb="MG G2O a 801 " ideal model delta sigma weight residual 2.065 2.362 -0.297 2.00e-02 2.50e+03 2.20e+02 ... (remaining 39085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 53187 4.41 - 8.81: 625 8.81 - 13.22: 118 13.22 - 17.62: 21 17.62 - 22.03: 146 Bond angle restraints: 54097 Sorted by residual: angle pdb=" NB BCL A 810 " pdb="MG BCL A 810 " pdb=" ND BCL A 810 " ideal model delta sigma weight residual 157.70 179.73 -22.03 2.51e+00 1.58e-01 7.68e+01 angle pdb=" NB BCL a 814 " pdb="MG BCL a 814 " pdb=" ND BCL a 814 " ideal model delta sigma weight residual 157.70 179.71 -22.01 2.51e+00 1.58e-01 7.67e+01 angle pdb=" NB BCL a 811 " pdb="MG BCL a 811 " pdb=" ND BCL a 811 " ideal model delta sigma weight residual 157.70 179.68 -21.98 2.51e+00 1.58e-01 7.65e+01 angle pdb=" NB BCL a 806 " pdb="MG BCL a 806 " pdb=" ND BCL a 806 " ideal model delta sigma weight residual 157.70 179.66 -21.96 2.51e+00 1.58e-01 7.63e+01 angle pdb=" NB BCL a 804 " pdb="MG BCL a 804 " pdb=" ND BCL a 804 " ideal model delta sigma weight residual 157.70 179.64 -21.95 2.51e+00 1.58e-01 7.63e+01 ... (remaining 54092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.77: 20179 32.77 - 65.53: 964 65.53 - 98.30: 114 98.30 - 131.06: 27 131.06 - 163.83: 7 Dihedral angle restraints: 21291 sinusoidal: 9917 harmonic: 11374 Sorted by residual: dihedral pdb=" CA PHE a 656 " pdb=" C PHE a 656 " pdb=" N LEU a 657 " pdb=" CA LEU a 657 " ideal model delta harmonic sigma weight residual 180.00 150.79 29.21 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" C1 BCL A 812 " pdb=" C2 BCL A 812 " pdb=" C3 BCL A 812 " pdb=" C5 BCL A 812 " ideal model delta sinusoidal sigma weight residual -180.00 -145.64 -34.36 1 8.00e+00 1.56e-02 2.62e+01 dihedral pdb=" CA ALA Z 327 " pdb=" C ALA Z 327 " pdb=" N PRO Z 328 " pdb=" CA PRO Z 328 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 21288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.140: 5362 1.140 - 2.281: 0 2.281 - 3.421: 14 3.421 - 4.561: 0 4.561 - 5.702: 2 Chirality restraints: 5378 Sorted by residual: chirality pdb=" C3C GS0 a 802 " pdb=" C2C GS0 a 802 " pdb=" C4C GS0 a 802 " pdb=" CAC GS0 a 802 " both_signs ideal model delta sigma weight residual False 2.77 -2.93 5.70 2.00e-01 2.50e+01 8.13e+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 -2.77 5.31 2.00e-01 2.50e+01 7.04e+02 chirality pdb=" CBD G2O a 801 " pdb=" CAD G2O a 801 " pdb=" CGD G2O a 801 " pdb=" CHA G2O a 801 " both_signs ideal model delta sigma weight residual False 2.80 -0.03 2.83 2.00e-01 2.50e+01 2.00e+02 ... (remaining 5375 not shown) Planarity restraints: 6624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 F26 A 816 " 0.305 2.00e-02 2.50e+03 4.09e-01 2.09e+03 pdb=" C19 F26 A 816 " -0.345 2.00e-02 2.50e+03 pdb=" C23 F26 A 816 " 0.175 2.00e-02 2.50e+03 pdb=" C24 F26 A 816 " -0.609 2.00e-02 2.50e+03 pdb=" C27 F26 A 816 " 0.473 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 F39 a 815 " 0.319 2.00e-02 2.50e+03 3.70e-01 1.71e+03 pdb=" C42 F39 a 815 " -0.278 2.00e-02 2.50e+03 pdb=" C43 F39 a 815 " 0.104 2.00e-02 2.50e+03 pdb=" C44 F39 a 815 " -0.565 2.00e-02 2.50e+03 pdb=" C51 F39 a 815 " 0.420 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 F26 a 816 " 0.107 2.00e-02 2.50e+03 3.23e-01 1.31e+03 pdb=" C17 F26 a 816 " -0.139 2.00e-02 2.50e+03 pdb=" C18 F26 a 816 " 0.568 2.00e-02 2.50e+03 pdb=" C22 F26 a 816 " -0.380 2.00e-02 2.50e+03 pdb=" C8 F26 a 816 " -0.156 2.00e-02 2.50e+03 ... (remaining 6621 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 111 2.39 - 3.02: 21176 3.02 - 3.65: 60383 3.65 - 4.27: 99234 4.27 - 4.90: 166167 Nonbonded interactions: 347071 Sorted by model distance: nonbonded pdb=" O GLY a 696 " pdb="CA CA a 823 " model vdw 1.767 2.510 nonbonded pdb=" OD2 ASP a 563 " pdb=" OE2 GLU a 603 " model vdw 1.939 3.040 nonbonded pdb=" OG SER W 73 " pdb=" OD1 ASN W 80 " model vdw 1.976 3.040 nonbonded pdb=" OG SER Z 332 " pdb=" O1 LHG Z 401 " model vdw 2.060 3.040 nonbonded pdb=" OH TYR Y 16 " pdb=" OBB BCL Y 404 " model vdw 2.060 3.040 ... (remaining 347066 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 708 or resid 803 through 807 or (resid 808 and \ (name NB or name ND or name 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 C4B or name C4C or name C4D or name CAA or name CAB or n \ ame CAC or name CAD or name 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 CMC or name CMD or name NA or name NC or name O1A or nam \ e O1D or name O2A or name O2D or name OBB or name OBD or name MG )) or resid 809 \ through 816 or (resid 818 and (name C1 or name C10 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C4 or name C5 or name C6 or name C \ 7 or name C8 or name C9 or name O1 or name O10 or name O2 or name O3 or name O4 \ or name O5 or name O6 or name O7 or name O8 or name O9 or name P )) or resid 819 \ or (resid 822 and (name C1 or name C10 or name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 o \ r name C28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C3 \ 3 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O1 or name O \ 10 or name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name O8 \ or name O9 )))) selection = (chain 'a' and (resid 59 through 708 or resid 803 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 )) or resid 815 through 816 or (resi \ d 818 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C2 \ 0 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or nam \ e C29 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ C9 or name O1 or name O10 or name O2 or name O3 or name O4 or name O5 or name O6 \ or name O7 or name O8 or name O9 or name P )) or resid 819 or (resid 822 and (n \ ame C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 o \ r name C16 or name C17 or name C18 or name C19 or name C2 or name C28 or name C2 \ 9 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name C39 or name C4 or name C5 or na \ me C6 or name C7 or name C8 or name C9 or name O1 or name O10 or name O2 or name \ O3 or name O4 or name O5 or name O6 or name O7 or name O8 or name O9 )))) } ncs_group { reference = (chain 'U' and (resid 10 through 366 or resid 402 through 407)) selection = (chain 'V' and (resid 10 through 366 or resid 402 through 406 or (resid 407 and \ (name NB or name ND or name 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 C4B or name C4C or name C4D or name CAA or name CAB or n \ ame CAC or name CAD or name 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 CMC or name CMD or name NA or name NC or name O1A or nam \ e O1D or name O2A or name O2D or name OBB or name OBD or name MG )))) selection = (chain 'W' and (resid 10 through 366 or resid 402 through 406 or (resid 407 and \ (name NB or name ND or name 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 C4B or name C4C or name C4D or name CAA or name CAB or n \ ame CAC or name CAD or name 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 CMC or name CMD or name NA or name NC or name O1A or nam \ e O1D or name O2A or name O2D or name OBB or name OBD or name MG )))) selection = (chain 'X' and (resid 10 through 366 or resid 402 through 407)) selection = (chain 'Y' and (resid 10 through 366 or resid 402 through 406 or (resid 407 and \ (name NB or name ND or name 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 C4B or name C4C or name C4D or name CAA or name CAB or n \ ame CAC or name CAD or name 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 CMC or name CMD or name NA or name NC or name O1A or nam \ e O1D or name O2A or name O2D or name OBB or name OBD or name MG )))) selection = (chain 'Z' and (resid 10 through 366 or resid 402 through 406 or (resid 407 and \ (name NB or name ND or name 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 C4B or name C4C or name C4D or name CAA or name CAB or n \ ame CAC or name CAD or name 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 CMC or name CMD or name NA or name NC or name O1A or nam \ e O1D or name O2A or name O2D or name OBB or name OBD or name MG )))) } 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: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 40.490 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.019 0.899 39144 Z= 1.334 Angle : 1.623 69.729 54136 Z= 0.615 Chirality : 0.183 5.702 5378 Planarity : 0.024 0.409 6624 Dihedral : 18.829 163.827 14041 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.31 % Favored : 94.62 % Rotamer: Outliers : 0.09 % Allowed : 12.22 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 3976 helix: 0.09 (0.14), residues: 1410 sheet: -0.89 (0.16), residues: 1004 loop : -1.26 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 143 TYR 0.021 0.001 TYR a 114 PHE 0.026 0.002 PHE A 692 TRP 0.018 0.001 TRP U 184 HIS 0.007 0.001 HIS W 227 Details of bonding type rmsd/Z covalent geometry : bond 0.01150 / 0.56 (39090) covalent geometry : angle 1.57950 / 0.61 (54097) hydrogen bonds : bond 0.12381 / 8.35 ( 1365) hydrogen bonds : angle 6.58847 / 4.87 ( 3972) metal coordination : bond 0.08010 / 6.40 ( 13) metal coordination : angle 13.96603 / 10.45 ( 39) Misc. bond : bond 0.48291 / 26.98 ( 41) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 796 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7757 (mptp) cc_final: 0.7394 (mtpp) REVERT: A 116 THR cc_start: 0.8331 (m) cc_final: 0.8064 (m) REVERT: A 127 ASP cc_start: 0.7118 (t0) cc_final: 0.6854 (t0) REVERT: A 224 MET cc_start: 0.7793 (mtm) cc_final: 0.7440 (mtp) REVERT: A 275 MET cc_start: 0.6929 (mtp) cc_final: 0.6564 (mtm) REVERT: A 311 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7382 (ttpt) REVERT: A 325 PHE cc_start: 0.8108 (p90) cc_final: 0.7697 (p90) REVERT: A 429 MET cc_start: 0.8005 (mtm) cc_final: 0.7803 (mtp) REVERT: a 96 SER cc_start: 0.7865 (t) cc_final: 0.7524 (m) REVERT: a 168 ASN cc_start: 0.8064 (t0) cc_final: 0.7838 (t0) REVERT: a 182 ASP cc_start: 0.7416 (t0) cc_final: 0.6753 (p0) REVERT: a 253 PHE cc_start: 0.7113 (m-80) cc_final: 0.6846 (m-80) REVERT: a 266 ASN cc_start: 0.5422 (m-40) cc_final: 0.4910 (m110) REVERT: a 414 LYS cc_start: 0.7936 (mptt) cc_final: 0.7604 (mmmt) REVERT: a 436 MET cc_start: 0.7596 (ttm) cc_final: 0.7374 (ttt) REVERT: a 585 ILE cc_start: 0.8336 (tp) cc_final: 0.8098 (pt) REVERT: B 171 ARG cc_start: 0.8145 (mmt180) cc_final: 0.7936 (mmt180) REVERT: B 172 CYS cc_start: 0.5904 (m) cc_final: 0.5336 (m) REVERT: B 181 SER cc_start: 0.6773 (m) cc_final: 0.6368 (t) REVERT: c 73 ILE cc_start: 0.6735 (tt) cc_final: 0.6477 (tt) REVERT: D 24 SER cc_start: 0.8711 (p) cc_final: 0.8480 (m) REVERT: E 58 LYS cc_start: 0.6072 (mmmm) cc_final: 0.4887 (mmtm) REVERT: U 52 LYS cc_start: 0.8023 (mttt) cc_final: 0.7549 (mptt) REVERT: U 147 ASP cc_start: 0.7788 (t0) cc_final: 0.7547 (t70) REVERT: U 224 ARG cc_start: 0.7941 (ptp-110) cc_final: 0.7698 (ptp-170) REVERT: V 81 LYS cc_start: 0.8421 (tttt) cc_final: 0.7480 (mtmm) REVERT: V 160 ILE cc_start: 0.8284 (mt) cc_final: 0.8051 (pt) REVERT: V 168 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7442 (mmtm) REVERT: W 50 ASP cc_start: 0.6974 (m-30) cc_final: 0.6604 (m-30) REVERT: W 52 LYS cc_start: 0.7814 (tptm) cc_final: 0.7554 (tppp) REVERT: W 74 ILE cc_start: 0.8264 (mt) cc_final: 0.7960 (mp) REVERT: W 118 SER cc_start: 0.7796 (p) cc_final: 0.7532 (p) REVERT: W 128 ASP cc_start: 0.6366 (p0) cc_final: 0.5933 (t0) REVERT: W 134 VAL cc_start: 0.7929 (t) cc_final: 0.7660 (p) REVERT: W 140 MET cc_start: 0.7786 (tpp) cc_final: 0.7554 (tpt) REVERT: W 255 GLU cc_start: 0.6577 (tt0) cc_final: 0.6042 (tt0) REVERT: X 52 LYS cc_start: 0.6789 (mttp) cc_final: 0.6404 (ptmm) REVERT: X 93 LYS cc_start: 0.7626 (ptpt) cc_final: 0.7125 (tppp) REVERT: X 99 VAL cc_start: 0.7702 (t) cc_final: 0.7434 (m) REVERT: X 167 VAL cc_start: 0.7846 (t) cc_final: 0.7571 (p) REVERT: X 186 ILE cc_start: 0.8644 (pt) cc_final: 0.8256 (tt) REVERT: X 347 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7539 (mtp180) REVERT: Y 52 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7686 (mttm) REVERT: Y 255 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6907 (mt-10) REVERT: Y 268 LYS cc_start: 0.7388 (tmmt) cc_final: 0.7150 (tttm) REVERT: Y 337 GLU cc_start: 0.6829 (mp0) cc_final: 0.6523 (mp0) REVERT: Z 58 LEU cc_start: 0.7660 (tp) cc_final: 0.7371 (tp) REVERT: Z 68 SER cc_start: 0.8450 (m) cc_final: 0.8079 (t) REVERT: Z 140 MET cc_start: 0.7809 (tpp) cc_final: 0.7350 (tpp) REVERT: Z 194 ASN cc_start: 0.6933 (t0) cc_final: 0.6680 (m110) outliers start: 3 outliers final: 3 residues processed: 799 average time/residue: 0.2616 time to fit residues: 329.3420 Evaluate side-chains 582 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 579 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain E residue 6 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 GLN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN a 150 HIS a 645 GLN a 662 ASN B 7 ASN c 39 HIS D 99 ASN U 90 ASN U 141 GLN ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 209 ASN U 305 ASN V 289 ASN V 298 HIS ** W 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 198 GLN W 312 GLN X 111 HIS ** X 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 306 ASN Z 90 ASN ** Z 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.169725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.152376 restraints weight = 46365.535| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.42 r_work: 0.3596 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.800 39144 Z= 0.254 Angle : 0.932 63.976 54136 Z= 0.357 Chirality : 0.046 0.266 5378 Planarity : 0.005 0.085 6624 Dihedral : 16.482 158.143 6840 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 2.85 % Allowed : 16.15 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 3976 helix: 0.14 (0.13), residues: 1440 sheet: -0.86 (0.17), residues: 1010 loop : -1.31 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Z 224 TYR 0.021 0.002 TYR U 364 PHE 0.037 0.002 PHE a 686 TRP 0.025 0.002 TRP U 184 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (39090) covalent geometry : angle 0.85947 / 0.36 (54097) hydrogen bonds : bond 0.04650 / 3.13 ( 1365) hydrogen bonds : angle 5.59256 / 4.13 ( 3972) metal coordination : bond 0.02133 / 1.33 ( 13) metal coordination : angle 13.48275 / 9.86 ( 39) Misc. bond : bond 0.19025 / 11.93 ( 41) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 650 time to evaluate : 1.104 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 60 LYS cc_start: 0.7929 (mptp) cc_final: 0.7535 (mtpp) REVERT: A 116 THR cc_start: 0.8434 (m) cc_final: 0.8171 (m) REVERT: A 127 ASP cc_start: 0.7006 (t0) cc_final: 0.6721 (t0) REVERT: A 245 MET cc_start: 0.8482 (mmm) cc_final: 0.8214 (mmm) REVERT: A 311 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7668 (ttpt) REVERT: A 401 ASN cc_start: 0.7996 (p0) cc_final: 0.7619 (p0) REVERT: A 471 PHE cc_start: 0.8799 (m-80) cc_final: 0.8450 (m-80) REVERT: A 590 HIS cc_start: 0.8009 (m90) cc_final: 0.7733 (m90) REVERT: a 96 SER cc_start: 0.7864 (t) cc_final: 0.7385 (m) REVERT: a 182 ASP cc_start: 0.7331 (t0) cc_final: 0.6875 (p0) REVERT: a 266 ASN cc_start: 0.5686 (m-40) cc_final: 0.5163 (m110) REVERT: a 318 PHE cc_start: 0.8265 (m-80) cc_final: 0.8043 (m-80) REVERT: a 414 LYS cc_start: 0.8174 (mptt) cc_final: 0.7807 (mmmt) REVERT: a 436 MET cc_start: 0.7886 (ttm) cc_final: 0.7680 (ttt) REVERT: a 469 PRO cc_start: 0.7753 (Cg_exo) cc_final: 0.7344 (Cg_endo) REVERT: a 472 GLN cc_start: 0.6949 (pm20) cc_final: 0.6581 (pm20) REVERT: a 664 ARG cc_start: 0.7664 (mtt90) cc_final: 0.7216 (mtp180) REVERT: B 171 ARG cc_start: 0.8342 (mmt180) cc_final: 0.7896 (mmt90) REVERT: B 181 SER cc_start: 0.6709 (m) cc_final: 0.6120 (t) REVERT: C 102 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7548 (mtpt) REVERT: c 69 MET cc_start: 0.7125 (tpt) cc_final: 0.6192 (tmm) REVERT: D 47 LEU cc_start: 0.5545 (OUTLIER) cc_final: 0.3950 (tt) REVERT: D 69 ARG cc_start: 0.7734 (mtp-110) cc_final: 0.7529 (mtp85) REVERT: D 115 ARG cc_start: 0.6424 (tpt170) cc_final: 0.5086 (mmm160) REVERT: U 52 LYS cc_start: 0.8351 (mttt) cc_final: 0.7868 (mptt) REVERT: U 193 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7342 (mp) REVERT: U 337 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7471 (tm-30) REVERT: V 81 LYS cc_start: 0.8738 (tttt) cc_final: 0.8476 (tptp) REVERT: V 160 ILE cc_start: 0.8415 (mt) cc_final: 0.8161 (pt) REVERT: V 168 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7661 (mmtm) REVERT: W 50 ASP cc_start: 0.7293 (m-30) cc_final: 0.6873 (m-30) REVERT: W 76 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: W 128 ASP cc_start: 0.6515 (p0) cc_final: 0.5941 (t0) REVERT: W 140 MET cc_start: 0.8207 (tpp) cc_final: 0.7964 (tpt) REVERT: W 255 GLU cc_start: 0.7085 (tt0) cc_final: 0.6591 (tt0) REVERT: W 306 ASN cc_start: 0.8397 (m-40) cc_final: 0.8171 (t0) REVERT: X 52 LYS cc_start: 0.7198 (mttp) cc_final: 0.6748 (ptmm) REVERT: X 74 ILE cc_start: 0.8311 (mp) cc_final: 0.8080 (mt) REVERT: X 99 VAL cc_start: 0.7595 (t) cc_final: 0.7299 (m) REVERT: X 149 LEU cc_start: 0.7677 (tt) cc_final: 0.7422 (tp) REVERT: X 167 VAL cc_start: 0.7941 (t) cc_final: 0.7641 (p) REVERT: X 198 GLN cc_start: 0.8110 (mt0) cc_final: 0.7733 (mt0) REVERT: X 232 MET cc_start: 0.7970 (ttm) cc_final: 0.7697 (ttp) REVERT: X 347 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7731 (mtp180) REVERT: Y 52 LYS cc_start: 0.8330 (ttmt) cc_final: 0.8044 (mttp) REVERT: Y 140 MET cc_start: 0.7599 (mmt) cc_final: 0.6325 (mtp) REVERT: Y 198 GLN cc_start: 0.7911 (tt0) cc_final: 0.7558 (mt0) REVERT: Y 268 LYS cc_start: 0.7530 (tmmt) cc_final: 0.7235 (tttm) REVERT: Z 31 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8207 (mptt) REVERT: Z 52 LYS cc_start: 0.8733 (mttt) cc_final: 0.8454 (mtmt) REVERT: Z 68 SER cc_start: 0.8527 (m) cc_final: 0.7980 (t) REVERT: Z 108 ASP cc_start: 0.6640 (m-30) cc_final: 0.6357 (m-30) REVERT: Z 140 MET cc_start: 0.8107 (tpp) cc_final: 0.7671 (tpp) REVERT: Z 194 ASN cc_start: 0.7502 (t0) cc_final: 0.6923 (m110) outliers start: 95 outliers final: 49 residues processed: 708 average time/residue: 0.2452 time to fit residues: 279.1301 Evaluate side-chains 625 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 572 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain a residue 341 SER Chi-restraints excluded: chain a residue 348 ASP Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 610 SER Chi-restraints excluded: chain a residue 700 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain U residue 90 ASN Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 161 ASP Chi-restraints excluded: chain U residue 186 ILE Chi-restraints excluded: chain U residue 193 LEU Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 221 SER Chi-restraints excluded: chain V residue 277 SER Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 159 LEU Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 198 GLN Chi-restraints excluded: chain W residue 267 VAL Chi-restraints excluded: chain X residue 95 ARG Chi-restraints excluded: chain X residue 173 THR Chi-restraints excluded: chain X residue 193 LEU Chi-restraints excluded: chain X residue 262 SER Chi-restraints excluded: chain X residue 323 ILE Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain Z residue 72 GLU Chi-restraints excluded: chain Z residue 104 VAL Chi-restraints excluded: chain Z residue 105 SER Chi-restraints excluded: chain Z residue 205 VAL Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 284 LEU Chi-restraints excluded: chain Z residue 335 LEU Chi-restraints excluded: chain Z residue 337 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 321 optimal weight: 5.9990 chunk 346 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 293 optimal weight: 7.9990 chunk 273 optimal weight: 0.0870 chunk 208 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 GLN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN B 166 GLN D 99 ASN ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 305 ASN ** W 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 198 GLN W 312 GLN ** X 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 HIS ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 289 ASN ** Y 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 306 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.168086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.150283 restraints weight = 46649.672| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.47 r_work: 0.3494 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.689 39144 Z= 0.200 Angle : 0.907 65.921 54136 Z= 0.340 Chirality : 0.045 0.218 5378 Planarity : 0.005 0.067 6624 Dihedral : 15.467 168.282 6839 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.70 % Rotamer: Outliers : 3.36 % Allowed : 17.80 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 3976 helix: 0.24 (0.14), residues: 1424 sheet: -0.87 (0.17), residues: 1007 loop : -1.26 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Z 224 TYR 0.024 0.002 TYR U 364 PHE 0.024 0.002 PHE A 686 TRP 0.027 0.002 TRP U 184 HIS 0.006 0.001 HIS W 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (39090) covalent geometry : angle 0.81691 / 0.34 (54097) hydrogen bonds : bond 0.04342 / 2.92 ( 1365) hydrogen bonds : angle 5.44980 / 4.03 ( 3972) metal coordination : bond 0.01949 / 1.23 ( 13) metal coordination : angle 14.68537 / 10.67 ( 39) Misc. bond : bond 0.15600 / 9.97 ( 41) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 634 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7856 (mptp) cc_final: 0.7371 (mtpp) REVERT: A 116 THR cc_start: 0.8531 (m) cc_final: 0.8212 (m) REVERT: A 127 ASP cc_start: 0.7067 (t0) cc_final: 0.6766 (t0) REVERT: A 222 ILE cc_start: 0.8424 (mm) cc_final: 0.8195 (mt) REVERT: A 224 MET cc_start: 0.8043 (mtp) cc_final: 0.7776 (mtp) REVERT: A 327 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.6575 (mtt90) REVERT: A 383 TYR cc_start: 0.8673 (m-10) cc_final: 0.8403 (m-10) REVERT: A 401 ASN cc_start: 0.7995 (p0) cc_final: 0.7666 (p0) REVERT: A 423 LYS cc_start: 0.8379 (mtpt) cc_final: 0.7729 (mttt) REVERT: A 471 PHE cc_start: 0.8746 (m-80) cc_final: 0.8312 (m-80) REVERT: A 514 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.7058 (p0) REVERT: A 682 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6931 (m-80) REVERT: a 88 PHE cc_start: 0.8302 (m-10) cc_final: 0.8018 (m-10) REVERT: a 90 MET cc_start: 0.8382 (mmt) cc_final: 0.8016 (mmm) REVERT: a 96 SER cc_start: 0.8012 (t) cc_final: 0.7531 (m) REVERT: a 151 PHE cc_start: 0.7486 (m-80) cc_final: 0.7283 (m-80) REVERT: a 168 ASN cc_start: 0.8540 (t0) cc_final: 0.8207 (t0) REVERT: a 182 ASP cc_start: 0.7500 (t0) cc_final: 0.6859 (p0) REVERT: a 253 PHE cc_start: 0.7527 (m-80) cc_final: 0.7253 (m-80) REVERT: a 266 ASN cc_start: 0.5674 (m-40) cc_final: 0.5237 (m110) REVERT: a 310 TYR cc_start: 0.8778 (m-80) cc_final: 0.7793 (m-80) REVERT: a 318 PHE cc_start: 0.8423 (m-80) cc_final: 0.8152 (m-80) REVERT: a 414 LYS cc_start: 0.8069 (mptt) cc_final: 0.7765 (mmmt) REVERT: a 436 MET cc_start: 0.8025 (ttm) cc_final: 0.7821 (ttt) REVERT: a 468 LEU cc_start: 0.7583 (mp) cc_final: 0.7369 (mt) REVERT: a 469 PRO cc_start: 0.7847 (Cg_exo) cc_final: 0.7363 (Cg_endo) REVERT: a 472 GLN cc_start: 0.6766 (pm20) cc_final: 0.6328 (pm20) REVERT: a 582 TRP cc_start: 0.8669 (m100) cc_final: 0.8459 (m100) REVERT: a 647 ARG cc_start: 0.7745 (mtt-85) cc_final: 0.7390 (mtt-85) REVERT: a 664 ARG cc_start: 0.7814 (mtt90) cc_final: 0.7184 (mtp180) REVERT: B 164 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6648 (t70) REVERT: B 171 ARG cc_start: 0.8232 (mmt180) cc_final: 0.7831 (mmt90) REVERT: B 181 SER cc_start: 0.6817 (m) cc_final: 0.6275 (t) REVERT: C 50 MET cc_start: 0.7725 (mmp) cc_final: 0.7525 (tpp) REVERT: C 102 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7491 (mtpt) REVERT: c 69 MET cc_start: 0.6988 (tpt) cc_final: 0.5845 (tmm) REVERT: c 90 MET cc_start: 0.4181 (OUTLIER) cc_final: 0.3534 (mtp) REVERT: D 47 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.3883 (tt) REVERT: D 115 ARG cc_start: 0.6100 (tpt170) cc_final: 0.4730 (mmm160) REVERT: U 52 LYS cc_start: 0.8322 (mttt) cc_final: 0.7732 (mptt) REVERT: U 209 ASN cc_start: 0.7277 (OUTLIER) cc_final: 0.7042 (p0) REVERT: U 242 LEU cc_start: 0.8321 (tp) cc_final: 0.8090 (mp) REVERT: U 337 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7086 (tm-30) REVERT: V 81 LYS cc_start: 0.8659 (tttt) cc_final: 0.8344 (tptp) REVERT: V 160 ILE cc_start: 0.8372 (mt) cc_final: 0.8045 (pt) REVERT: V 168 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7437 (mmtm) REVERT: W 50 ASP cc_start: 0.7304 (m-30) cc_final: 0.6841 (m-30) REVERT: W 76 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: W 134 VAL cc_start: 0.7887 (t) cc_final: 0.7583 (p) REVERT: W 140 MET cc_start: 0.8271 (tpp) cc_final: 0.7974 (tpt) REVERT: W 255 GLU cc_start: 0.7064 (tt0) cc_final: 0.6644 (tt0) REVERT: W 306 ASN cc_start: 0.8368 (m-40) cc_final: 0.8140 (t0) REVERT: X 17 GLU cc_start: 0.6763 (tp30) cc_final: 0.6397 (tp30) REVERT: X 52 LYS cc_start: 0.7268 (mttp) cc_final: 0.6535 (ptmm) REVERT: X 99 VAL cc_start: 0.7685 (t) cc_final: 0.7328 (m) REVERT: X 121 ASN cc_start: 0.8506 (t0) cc_final: 0.8134 (t0) REVERT: X 149 LEU cc_start: 0.7613 (tt) cc_final: 0.7394 (tp) REVERT: X 167 VAL cc_start: 0.7863 (t) cc_final: 0.7567 (p) REVERT: X 232 MET cc_start: 0.7938 (ttm) cc_final: 0.7685 (ttp) REVERT: X 253 GLN cc_start: 0.6877 (tm-30) cc_final: 0.6218 (tm-30) REVERT: X 347 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7677 (mtp180) REVERT: Y 52 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7794 (mttp) REVERT: Y 73 SER cc_start: 0.8481 (p) cc_final: 0.8181 (m) REVERT: Y 85 GLU cc_start: 0.6961 (tt0) cc_final: 0.6633 (mp0) REVERT: Y 140 MET cc_start: 0.7714 (mmt) cc_final: 0.7347 (mmm) REVERT: Y 198 GLN cc_start: 0.7751 (tt0) cc_final: 0.7312 (mt0) REVERT: Y 268 LYS cc_start: 0.7673 (tmmt) cc_final: 0.7228 (tttm) REVERT: Z 31 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8236 (mptt) REVERT: Z 52 LYS cc_start: 0.8616 (mttt) cc_final: 0.8225 (mtmt) REVERT: Z 68 SER cc_start: 0.8432 (m) cc_final: 0.7979 (t) REVERT: Z 71 PHE cc_start: 0.8492 (m-80) cc_final: 0.8213 (m-80) REVERT: Z 140 MET cc_start: 0.8165 (tpp) cc_final: 0.7534 (tpp) REVERT: Z 190 PHE cc_start: 0.8185 (t80) cc_final: 0.7949 (t80) REVERT: Z 194 ASN cc_start: 0.7495 (t0) cc_final: 0.6845 (m110) REVERT: Z 272 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7063 (tp30) REVERT: Z 310 ASP cc_start: 0.7771 (t0) cc_final: 0.7462 (t70) outliers start: 112 outliers final: 60 residues processed: 705 average time/residue: 0.2334 time to fit residues: 265.0985 Evaluate side-chains 665 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 595 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 341 SER Chi-restraints excluded: chain a residue 355 LEU Chi-restraints excluded: chain a residue 358 SER Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 610 SER Chi-restraints excluded: chain a residue 700 THR Chi-restraints excluded: chain a residue 708 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 186 ILE Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 221 SER Chi-restraints excluded: chain V residue 277 SER Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 159 LEU Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 198 GLN Chi-restraints excluded: chain W residue 267 VAL Chi-restraints excluded: chain W residue 293 ILE Chi-restraints excluded: chain W residue 357 VAL Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 173 THR Chi-restraints excluded: chain X residue 262 SER Chi-restraints excluded: chain X residue 323 ILE Chi-restraints excluded: chain Y residue 103 MET Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Y residue 150 MET Chi-restraints excluded: chain Y residue 309 VAL Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain Z residue 54 ASN Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain Z residue 104 VAL Chi-restraints excluded: chain Z residue 105 SER Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 205 VAL Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 246 ASP Chi-restraints excluded: chain Z residue 272 GLU Chi-restraints excluded: chain Z residue 284 LEU Chi-restraints excluded: chain Z residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 105 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 230 optimal weight: 0.0270 chunk 106 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 213 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 272 ASN D 99 ASN ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 305 ASN V 156 ASN W 121 ASN X 206 ASN Y 13 HIS Y 141 GLN ** Y 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.169164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.150699 restraints weight = 46393.077| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.55 r_work: 0.3498 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.663 39144 Z= 0.159 Angle : 0.867 64.846 54136 Z= 0.322 Chirality : 0.044 0.217 5378 Planarity : 0.004 0.066 6624 Dihedral : 14.723 177.831 6839 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 3.45 % Allowed : 18.85 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.98 (0.13), residues: 3976 helix: 0.29 (0.14), residues: 1430 sheet: -0.81 (0.17), residues: 1000 loop : -1.30 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Z 131 TYR 0.024 0.001 TYR U 364 PHE 0.021 0.001 PHE A 686 TRP 0.026 0.001 TRP U 184 HIS 0.005 0.001 HIS W 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (39090) covalent geometry : angle 0.77050 / 0.32 (54097) hydrogen bonds : bond 0.04080 / 2.74 ( 1365) hydrogen bonds : angle 5.30004 / 3.92 ( 3972) metal coordination : bond 0.01574 / 1.04 ( 13) metal coordination : angle 14.84218 / 10.75 ( 39) Misc. bond : bond 0.15095 / 9.55 ( 41) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 625 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7921 (mptp) cc_final: 0.7467 (mtpp) REVERT: A 127 ASP cc_start: 0.7022 (t0) cc_final: 0.6727 (t0) REVERT: A 222 ILE cc_start: 0.8412 (mm) cc_final: 0.8200 (mt) REVERT: A 224 MET cc_start: 0.8091 (mtp) cc_final: 0.7824 (mtp) REVERT: A 311 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7687 (ttpt) REVERT: A 327 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7599 (mtt90) REVERT: A 408 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7786 (mmmt) REVERT: A 471 PHE cc_start: 0.8731 (m-80) cc_final: 0.8248 (m-80) REVERT: A 514 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6966 (p0) REVERT: A 682 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6883 (m-80) REVERT: a 88 PHE cc_start: 0.8337 (m-10) cc_final: 0.8014 (m-10) REVERT: a 96 SER cc_start: 0.7947 (t) cc_final: 0.7547 (m) REVERT: a 111 ASN cc_start: 0.8482 (p0) cc_final: 0.8255 (p0) REVERT: a 151 PHE cc_start: 0.7471 (m-80) cc_final: 0.7076 (m-80) REVERT: a 168 ASN cc_start: 0.8557 (t0) cc_final: 0.8257 (t0) REVERT: a 182 ASP cc_start: 0.7411 (t0) cc_final: 0.6883 (p0) REVERT: a 253 PHE cc_start: 0.7674 (m-80) cc_final: 0.7412 (m-80) REVERT: a 266 ASN cc_start: 0.5980 (m-40) cc_final: 0.5584 (m110) REVERT: a 310 TYR cc_start: 0.8827 (m-80) cc_final: 0.7723 (m-80) REVERT: a 318 PHE cc_start: 0.8531 (m-80) cc_final: 0.8294 (m-80) REVERT: a 414 LYS cc_start: 0.8120 (mptt) cc_final: 0.7761 (mmmt) REVERT: a 469 PRO cc_start: 0.7888 (Cg_exo) cc_final: 0.7423 (Cg_endo) REVERT: a 472 GLN cc_start: 0.6919 (pm20) cc_final: 0.6450 (pm20) REVERT: a 548 MET cc_start: 0.8270 (mtp) cc_final: 0.7988 (mtp) REVERT: a 647 ARG cc_start: 0.7792 (mtt-85) cc_final: 0.7508 (mtt-85) REVERT: a 664 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7171 (mtp180) REVERT: B 171 ARG cc_start: 0.8236 (mmt180) cc_final: 0.7925 (mmt90) REVERT: B 181 SER cc_start: 0.6825 (m) cc_final: 0.6310 (t) REVERT: C 46 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8518 (mm) REVERT: C 79 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7773 (mp) REVERT: C 102 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7565 (mtpt) REVERT: c 69 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.5905 (tmm) REVERT: c 90 MET cc_start: 0.3936 (OUTLIER) cc_final: 0.3364 (mtp) REVERT: D 47 LEU cc_start: 0.5535 (OUTLIER) cc_final: 0.3826 (tt) REVERT: D 115 ARG cc_start: 0.6089 (tpt170) cc_final: 0.4709 (mmm-85) REVERT: E 25 GLU cc_start: 0.7307 (pp20) cc_final: 0.6804 (pp20) REVERT: E 29 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6986 (mt) REVERT: U 52 LYS cc_start: 0.8319 (mttt) cc_final: 0.7772 (mptt) REVERT: U 209 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.7061 (p0) REVERT: U 247 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7414 (mmmt) REVERT: U 312 GLN cc_start: 0.8638 (tt0) cc_final: 0.8216 (tp40) REVERT: U 337 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7299 (tm-30) REVERT: V 81 LYS cc_start: 0.8725 (tttt) cc_final: 0.8452 (tptp) REVERT: V 156 ASN cc_start: 0.8544 (m-40) cc_final: 0.8333 (m110) REVERT: V 160 ILE cc_start: 0.8383 (mt) cc_final: 0.8055 (pt) REVERT: V 168 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7492 (mmtm) REVERT: W 50 ASP cc_start: 0.7348 (m-30) cc_final: 0.6910 (m-30) REVERT: W 76 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: W 94 GLU cc_start: 0.7254 (mp0) cc_final: 0.6904 (mp0) REVERT: W 121 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.8149 (t0) REVERT: W 134 VAL cc_start: 0.7942 (t) cc_final: 0.7673 (p) REVERT: W 242 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8048 (mp) REVERT: X 52 LYS cc_start: 0.7394 (mttp) cc_final: 0.6662 (ptmm) REVERT: X 95 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8000 (ttm-80) REVERT: X 99 VAL cc_start: 0.7643 (t) cc_final: 0.7331 (m) REVERT: X 121 ASN cc_start: 0.8443 (t0) cc_final: 0.8066 (t0) REVERT: X 232 MET cc_start: 0.7875 (ttm) cc_final: 0.7641 (ttp) REVERT: X 347 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7750 (mtp180) REVERT: Y 52 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7850 (mttp) REVERT: Y 73 SER cc_start: 0.8456 (p) cc_final: 0.8162 (m) REVERT: Y 85 GLU cc_start: 0.6938 (tt0) cc_final: 0.6693 (mp0) REVERT: Y 140 MET cc_start: 0.7677 (mmt) cc_final: 0.6194 (mtp) REVERT: Y 141 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: Y 198 GLN cc_start: 0.7720 (tt0) cc_final: 0.7321 (mt0) REVERT: Y 268 LYS cc_start: 0.7572 (tmmt) cc_final: 0.7223 (tttm) REVERT: Y 317 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7328 (mm) REVERT: Z 52 LYS cc_start: 0.8677 (mttt) cc_final: 0.8307 (mtmt) REVERT: Z 68 SER cc_start: 0.8424 (m) cc_final: 0.8006 (t) REVERT: Z 71 PHE cc_start: 0.8517 (m-80) cc_final: 0.8188 (m-80) REVERT: Z 140 MET cc_start: 0.8138 (tpp) cc_final: 0.7508 (tpp) REVERT: Z 190 PHE cc_start: 0.8261 (t80) cc_final: 0.8054 (t80) REVERT: Z 194 ASN cc_start: 0.7519 (t0) cc_final: 0.6887 (m110) REVERT: Z 195 GLU cc_start: 0.7794 (mp0) cc_final: 0.7536 (mp0) REVERT: Z 272 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7111 (tp30) REVERT: Z 310 ASP cc_start: 0.7893 (t0) cc_final: 0.7681 (t0) REVERT: Z 339 ARG cc_start: 0.8238 (ttp-170) cc_final: 0.7754 (ttp-170) outliers start: 115 outliers final: 57 residues processed: 696 average time/residue: 0.2288 time to fit residues: 257.9947 Evaluate side-chains 658 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 583 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 341 SER Chi-restraints excluded: chain a residue 355 LEU Chi-restraints excluded: chain a residue 465 LEU Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 542 ASP Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 610 SER Chi-restraints excluded: chain a residue 700 THR Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain c residue 69 MET Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 186 ILE Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 221 SER Chi-restraints excluded: chain V residue 277 SER Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 121 ASN Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 242 LEU Chi-restraints excluded: chain W residue 267 VAL Chi-restraints excluded: chain W residue 357 VAL Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 95 ARG Chi-restraints excluded: chain X residue 173 THR Chi-restraints excluded: chain X residue 262 SER Chi-restraints excluded: chain X residue 317 LEU Chi-restraints excluded: chain X residue 323 ILE Chi-restraints excluded: chain Y residue 103 MET Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 141 GLN Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Y residue 317 LEU Chi-restraints excluded: chain Y residue 350 GLU Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 54 ASN Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain Z residue 104 VAL Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 246 ASP Chi-restraints excluded: chain Z residue 255 GLU Chi-restraints excluded: chain Z residue 272 GLU Chi-restraints excluded: chain Z residue 335 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 87 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 374 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN U 90 ASN ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 209 ASN U 305 ASN W 121 ASN ** W 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 198 GLN W 305 ASN ** X 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 334 ASN Y 13 HIS ** Y 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.165917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.148159 restraints weight = 46636.441| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.46 r_work: 0.3509 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.634 39144 Z= 0.227 Angle : 0.916 65.492 54136 Z= 0.341 Chirality : 0.046 0.270 5378 Planarity : 0.005 0.065 6624 Dihedral : 14.400 175.861 6839 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 4.17 % Allowed : 19.03 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 3976 helix: 0.20 (0.13), residues: 1437 sheet: -0.88 (0.17), residues: 1010 loop : -1.34 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Z 224 TYR 0.025 0.002 TYR U 364 PHE 0.026 0.002 PHE A 686 TRP 0.033 0.002 TRP U 184 HIS 0.007 0.001 HIS W 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (39090) covalent geometry : angle 0.82225 / 0.34 (54097) hydrogen bonds : bond 0.04274 / 2.87 ( 1365) hydrogen bonds : angle 5.34226 / 3.96 ( 3972) metal coordination : bond 0.02002 / 1.23 ( 13) metal coordination : angle 15.06855 / 10.90 ( 39) Misc. bond : bond 0.13766 / 8.87 ( 41) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 637 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7968 (mptp) cc_final: 0.7613 (mtpp) REVERT: A 127 ASP cc_start: 0.7038 (t0) cc_final: 0.6778 (t0) REVERT: A 327 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7651 (mtt90) REVERT: A 408 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7882 (mmmt) REVERT: A 423 LYS cc_start: 0.8214 (mttt) cc_final: 0.8013 (mttt) REVERT: A 471 PHE cc_start: 0.8768 (m-80) cc_final: 0.8328 (m-80) REVERT: A 514 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7121 (p0) REVERT: A 516 LEU cc_start: 0.8576 (mp) cc_final: 0.8316 (mt) REVERT: A 682 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6982 (m-80) REVERT: a 88 PHE cc_start: 0.8383 (m-10) cc_final: 0.8032 (m-10) REVERT: a 90 MET cc_start: 0.8239 (mmm) cc_final: 0.7938 (mmt) REVERT: a 96 SER cc_start: 0.7992 (t) cc_final: 0.7514 (m) REVERT: a 151 PHE cc_start: 0.7401 (m-80) cc_final: 0.7032 (m-80) REVERT: a 168 ASN cc_start: 0.8671 (t0) cc_final: 0.8371 (t0) REVERT: a 182 ASP cc_start: 0.7407 (t0) cc_final: 0.6955 (p0) REVERT: a 245 MET cc_start: 0.8770 (tpt) cc_final: 0.8570 (tpp) REVERT: a 253 PHE cc_start: 0.7649 (m-80) cc_final: 0.7432 (m-80) REVERT: a 266 ASN cc_start: 0.6125 (m-40) cc_final: 0.5843 (m110) REVERT: a 310 TYR cc_start: 0.8854 (m-80) cc_final: 0.7786 (m-80) REVERT: a 414 LYS cc_start: 0.8140 (mptt) cc_final: 0.7803 (mmmt) REVERT: a 418 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6199 (tt0) REVERT: a 469 PRO cc_start: 0.7920 (Cg_exo) cc_final: 0.7529 (Cg_endo) REVERT: a 472 GLN cc_start: 0.6999 (pm20) cc_final: 0.6610 (pm20) REVERT: a 560 TRP cc_start: 0.7862 (m-10) cc_final: 0.7409 (m100) REVERT: a 647 ARG cc_start: 0.7922 (mtt-85) cc_final: 0.7638 (mtt-85) REVERT: a 664 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7382 (mtp180) REVERT: B 164 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6851 (t70) REVERT: B 171 ARG cc_start: 0.8271 (mmt180) cc_final: 0.7937 (mmt90) REVERT: B 181 SER cc_start: 0.6900 (m) cc_final: 0.6587 (p) REVERT: C 46 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8712 (mm) REVERT: C 79 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7819 (mp) REVERT: C 102 LYS cc_start: 0.8312 (mtmt) cc_final: 0.7738 (mtpt) REVERT: c 69 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.5737 (tmm) REVERT: c 90 MET cc_start: 0.3903 (OUTLIER) cc_final: 0.3333 (mtp) REVERT: D 115 ARG cc_start: 0.6177 (tpt170) cc_final: 0.4809 (mmm-85) REVERT: E 25 GLU cc_start: 0.7286 (pp20) cc_final: 0.6833 (pp20) REVERT: F 18 MET cc_start: 0.7613 (tpp) cc_final: 0.7194 (mmt) REVERT: U 29 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7922 (tttm) REVERT: U 52 LYS cc_start: 0.8330 (mttt) cc_final: 0.7854 (mptt) REVERT: U 209 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.7171 (p0) REVERT: U 337 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7462 (tm-30) REVERT: V 67 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8739 (mt) REVERT: V 81 LYS cc_start: 0.8802 (tttt) cc_final: 0.8554 (tptp) REVERT: V 160 ILE cc_start: 0.8538 (mt) cc_final: 0.8217 (pt) REVERT: V 168 LYS cc_start: 0.7911 (mtpt) cc_final: 0.7615 (mmtm) REVERT: W 50 ASP cc_start: 0.7488 (m-30) cc_final: 0.7019 (m-30) REVERT: W 94 GLU cc_start: 0.7162 (mp0) cc_final: 0.6866 (mp0) REVERT: W 134 VAL cc_start: 0.7996 (t) cc_final: 0.7737 (p) REVERT: W 242 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8149 (mp) REVERT: X 52 LYS cc_start: 0.7362 (mttp) cc_final: 0.6733 (ptmm) REVERT: X 95 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7997 (ttm-80) REVERT: X 99 VAL cc_start: 0.7792 (t) cc_final: 0.7482 (m) REVERT: X 193 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7872 (mm) REVERT: X 232 MET cc_start: 0.7864 (ttm) cc_final: 0.7635 (ttp) REVERT: X 347 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7804 (mtp180) REVERT: Y 52 LYS cc_start: 0.8375 (ttmt) cc_final: 0.7996 (mttm) REVERT: Y 141 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: Y 178 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: Y 198 GLN cc_start: 0.7754 (tt0) cc_final: 0.7376 (mt0) REVERT: Y 268 LYS cc_start: 0.7548 (tmmt) cc_final: 0.7285 (tttm) REVERT: Y 317 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7455 (mm) REVERT: Z 31 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8165 (mptt) REVERT: Z 52 LYS cc_start: 0.8713 (mttt) cc_final: 0.8216 (mtmt) REVERT: Z 68 SER cc_start: 0.8417 (m) cc_final: 0.8089 (t) REVERT: Z 140 MET cc_start: 0.8228 (tpp) cc_final: 0.7618 (tpp) REVERT: Z 194 ASN cc_start: 0.7509 (t0) cc_final: 0.6931 (m110) REVERT: Z 195 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: Z 272 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7114 (tp30) REVERT: Z 310 ASP cc_start: 0.7880 (t0) cc_final: 0.7663 (t0) outliers start: 139 outliers final: 84 residues processed: 721 average time/residue: 0.2299 time to fit residues: 269.0079 Evaluate side-chains 715 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 610 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 128 THR Chi-restraints excluded: chain a residue 157 LEU Chi-restraints excluded: chain a residue 341 SER Chi-restraints excluded: chain a residue 355 LEU Chi-restraints excluded: chain a residue 358 SER Chi-restraints excluded: chain a residue 418 GLN Chi-restraints excluded: chain a residue 465 LEU Chi-restraints excluded: chain a residue 509 THR Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 542 ASP Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 610 SER Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain a residue 700 THR Chi-restraints excluded: chain a residue 708 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain c residue 69 MET Chi-restraints excluded: chain c residue 78 PHE Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 90 ASN Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 186 ILE Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 184 TRP Chi-restraints excluded: chain V residue 200 ILE Chi-restraints excluded: chain V residue 221 SER Chi-restraints excluded: chain V residue 277 SER Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 198 GLN Chi-restraints excluded: chain W residue 200 ILE Chi-restraints excluded: chain W residue 224 ARG Chi-restraints excluded: chain W residue 242 LEU Chi-restraints excluded: chain W residue 267 VAL Chi-restraints excluded: chain W residue 288 LEU Chi-restraints excluded: chain W residue 305 ASN Chi-restraints excluded: chain W residue 357 VAL Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 95 ARG Chi-restraints excluded: chain X residue 173 THR Chi-restraints excluded: chain X residue 193 LEU Chi-restraints excluded: chain X residue 253 GLN Chi-restraints excluded: chain X residue 262 SER Chi-restraints excluded: chain X residue 323 ILE Chi-restraints excluded: chain Y residue 103 MET Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 141 GLN Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Y residue 178 ASP Chi-restraints excluded: chain Y residue 317 LEU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain Z residue 54 ASN Chi-restraints excluded: chain Z residue 104 VAL Chi-restraints excluded: chain Z residue 105 SER Chi-restraints excluded: chain Z residue 138 ILE Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 205 VAL Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 246 ASP Chi-restraints excluded: chain Z residue 272 GLU Chi-restraints excluded: chain Z residue 309 VAL Chi-restraints excluded: chain Z residue 335 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 84 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 chunk 346 optimal weight: 0.2980 chunk 100 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 228 optimal weight: 3.9990 chunk 338 optimal weight: 4.9990 chunk 27 optimal weight: 0.0770 chunk 357 optimal weight: 10.0000 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN ** a 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 587 HIS D 99 ASN U 90 ASN ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 156 ASN ** V 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 GLN V 289 ASN ** W 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 334 ASN Y 13 HIS ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.167278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148944 restraints weight = 46567.312| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.53 r_work: 0.3470 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.612 39144 Z= 0.174 Angle : 0.882 64.319 54136 Z= 0.324 Chirality : 0.044 0.209 5378 Planarity : 0.004 0.063 6624 Dihedral : 14.142 174.316 6839 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.60 % Favored : 95.35 % Rotamer: Outliers : 3.78 % Allowed : 20.17 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 3976 helix: 0.27 (0.14), residues: 1443 sheet: -0.87 (0.17), residues: 1004 loop : -1.33 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Z 224 TYR 0.027 0.002 TYR a 94 PHE 0.024 0.002 PHE X 183 TRP 0.029 0.001 TRP U 184 HIS 0.006 0.001 HIS W 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (39090) covalent geometry : angle 0.77943 / 0.32 (54097) hydrogen bonds : bond 0.04063 / 2.73 ( 1365) hydrogen bonds : angle 5.26093 / 3.90 ( 3972) metal coordination : bond 0.01698 / 1.08 ( 13) metal coordination : angle 15.37353 / 11.11 ( 39) Misc. bond : bond 0.14259 / 9.12 ( 41) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 628 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7925 (mptp) cc_final: 0.7316 (mtpp) REVERT: A 127 ASP cc_start: 0.7081 (t0) cc_final: 0.6759 (t0) REVERT: A 224 MET cc_start: 0.7851 (mtp) cc_final: 0.7642 (mtp) REVERT: A 327 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7603 (mtt90) REVERT: A 364 MET cc_start: 0.8759 (tpp) cc_final: 0.8536 (tpp) REVERT: A 408 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7814 (mmmt) REVERT: A 471 PHE cc_start: 0.8768 (m-80) cc_final: 0.8305 (m-80) REVERT: A 514 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7074 (p0) REVERT: A 516 LEU cc_start: 0.8479 (mp) cc_final: 0.8266 (mt) REVERT: A 682 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6952 (m-80) REVERT: a 88 PHE cc_start: 0.8400 (m-10) cc_final: 0.8019 (m-10) REVERT: a 96 SER cc_start: 0.7984 (t) cc_final: 0.7465 (m) REVERT: a 151 PHE cc_start: 0.7392 (m-80) cc_final: 0.6936 (m-80) REVERT: a 168 ASN cc_start: 0.8609 (t0) cc_final: 0.8280 (t0) REVERT: a 182 ASP cc_start: 0.7434 (t0) cc_final: 0.6908 (p0) REVERT: a 245 MET cc_start: 0.8762 (tpt) cc_final: 0.8550 (tpp) REVERT: a 253 PHE cc_start: 0.7638 (m-80) cc_final: 0.7418 (m-80) REVERT: a 266 ASN cc_start: 0.6138 (m-40) cc_final: 0.5845 (m110) REVERT: a 310 TYR cc_start: 0.8833 (m-80) cc_final: 0.7911 (m-80) REVERT: a 414 LYS cc_start: 0.7977 (mptt) cc_final: 0.7707 (mmmt) REVERT: a 469 PRO cc_start: 0.7944 (Cg_exo) cc_final: 0.7565 (Cg_endo) REVERT: a 472 GLN cc_start: 0.6788 (pm20) cc_final: 0.6428 (pm20) REVERT: a 528 LEU cc_start: 0.8624 (mt) cc_final: 0.8288 (mp) REVERT: a 647 ARG cc_start: 0.7822 (mtt-85) cc_final: 0.7527 (mtt-85) REVERT: a 664 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7250 (mtp180) REVERT: B 164 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6572 (t70) REVERT: B 171 ARG cc_start: 0.8240 (mmt180) cc_final: 0.7964 (mmt90) REVERT: B 181 SER cc_start: 0.6874 (m) cc_final: 0.6461 (t) REVERT: C 46 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8587 (mm) REVERT: C 50 MET cc_start: 0.7873 (mmp) cc_final: 0.7644 (mpp) REVERT: C 79 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7837 (mp) REVERT: C 102 LYS cc_start: 0.8361 (mtmt) cc_final: 0.7705 (mtpt) REVERT: c 69 MET cc_start: 0.6702 (tpt) cc_final: 0.5707 (tmm) REVERT: c 90 MET cc_start: 0.3787 (OUTLIER) cc_final: 0.3178 (mtp) REVERT: D 69 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7602 (mtp85) REVERT: E 25 GLU cc_start: 0.7173 (pp20) cc_final: 0.6706 (pp20) REVERT: F 18 MET cc_start: 0.7525 (tpp) cc_final: 0.7101 (mmt) REVERT: U 29 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7810 (mtmm) REVERT: U 52 LYS cc_start: 0.8286 (mttt) cc_final: 0.7735 (mptt) REVERT: U 141 GLN cc_start: 0.7477 (mp10) cc_final: 0.7271 (mp10) REVERT: U 337 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7544 (tm-30) REVERT: V 81 LYS cc_start: 0.8773 (tttt) cc_final: 0.8469 (tptp) REVERT: V 159 LEU cc_start: 0.8515 (mt) cc_final: 0.8268 (mt) REVERT: V 160 ILE cc_start: 0.8478 (mt) cc_final: 0.8124 (pt) REVERT: V 168 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7550 (mmtm) REVERT: W 50 ASP cc_start: 0.7440 (m-30) cc_final: 0.6964 (m-30) REVERT: W 94 GLU cc_start: 0.7241 (mp0) cc_final: 0.6882 (mp0) REVERT: W 242 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8048 (mp) REVERT: W 253 GLN cc_start: 0.7839 (tt0) cc_final: 0.7631 (mt0) REVERT: X 17 GLU cc_start: 0.6737 (tp30) cc_final: 0.6429 (tp30) REVERT: X 37 ASN cc_start: 0.7068 (m110) cc_final: 0.6768 (p0) REVERT: X 52 LYS cc_start: 0.7270 (mttp) cc_final: 0.6559 (ptmm) REVERT: X 95 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7699 (ttt90) REVERT: X 99 VAL cc_start: 0.7745 (t) cc_final: 0.7398 (m) REVERT: X 193 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7791 (mm) REVERT: X 232 MET cc_start: 0.7841 (ttm) cc_final: 0.7577 (ttp) REVERT: X 285 ARG cc_start: 0.7331 (mtp85) cc_final: 0.6861 (ttm-80) REVERT: X 347 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7725 (mtp180) REVERT: Y 52 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7830 (mttm) REVERT: Y 198 GLN cc_start: 0.7714 (tt0) cc_final: 0.7310 (mt0) REVERT: Y 255 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7513 (mt-10) REVERT: Y 268 LYS cc_start: 0.7592 (tmmt) cc_final: 0.7234 (tttm) REVERT: Z 31 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8200 (mptt) REVERT: Z 52 LYS cc_start: 0.8482 (mttt) cc_final: 0.8153 (mtmt) REVERT: Z 68 SER cc_start: 0.8518 (m) cc_final: 0.8180 (t) REVERT: Z 71 PHE cc_start: 0.8492 (m-80) cc_final: 0.8207 (m-80) REVERT: Z 140 MET cc_start: 0.8249 (tpp) cc_final: 0.7573 (tpp) REVERT: Z 194 ASN cc_start: 0.7458 (t0) cc_final: 0.6838 (m110) REVERT: Z 195 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: Z 255 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6889 (mm-30) REVERT: Z 272 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7166 (tp30) REVERT: Z 310 ASP cc_start: 0.7883 (t0) cc_final: 0.7681 (t0) outliers start: 126 outliers final: 76 residues processed: 706 average time/residue: 0.2258 time to fit residues: 259.6453 Evaluate side-chains 684 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 594 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 128 THR Chi-restraints excluded: chain a residue 157 LEU Chi-restraints excluded: chain a residue 341 SER Chi-restraints excluded: chain a residue 358 SER Chi-restraints excluded: chain a residue 465 LEU Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 542 ASP Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 610 SER Chi-restraints excluded: chain a residue 688 LEU Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain a residue 700 THR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 90 ASN Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 186 ILE Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 184 TRP Chi-restraints excluded: chain V residue 221 SER Chi-restraints excluded: chain V residue 277 SER Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 242 LEU Chi-restraints excluded: chain W residue 357 VAL Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 76 ASP Chi-restraints excluded: chain X residue 95 ARG Chi-restraints excluded: chain X residue 173 THR Chi-restraints excluded: chain X residue 193 LEU Chi-restraints excluded: chain X residue 253 GLN Chi-restraints excluded: chain X residue 262 SER Chi-restraints excluded: chain X residue 317 LEU Chi-restraints excluded: chain X residue 323 ILE Chi-restraints excluded: chain X residue 334 ASN Chi-restraints excluded: chain Y residue 103 MET Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain Z residue 54 ASN Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 104 VAL Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 246 ASP Chi-restraints excluded: chain Z residue 272 GLU Chi-restraints excluded: chain Z residue 293 ILE Chi-restraints excluded: chain Z residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 185 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 371 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 175 optimal weight: 0.5980 chunk 148 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 393 GLN a 587 HIS D 99 ASN ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 209 ASN ** V 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 198 GLN X 121 ASN ** X 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 HIS ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.164272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.146422 restraints weight = 46732.235| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.42 r_work: 0.3442 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.595 39144 Z= 0.246 Angle : 0.931 65.463 54136 Z= 0.346 Chirality : 0.046 0.389 5378 Planarity : 0.005 0.062 6624 Dihedral : 14.169 165.306 6839 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.69 % Rotamer: Outliers : 4.05 % Allowed : 19.81 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 3976 helix: 0.14 (0.13), residues: 1444 sheet: -0.91 (0.17), residues: 1012 loop : -1.33 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Z 224 TYR 0.041 0.002 TYR a 202 PHE 0.027 0.002 PHE A 686 TRP 0.035 0.002 TRP U 184 HIS 0.007 0.001 HIS W 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.25 (39090) covalent geometry : angle 0.83389 / 0.34 (54097) hydrogen bonds : bond 0.04296 / 2.87 ( 1365) hydrogen bonds : angle 5.37311 / 3.97 ( 3972) metal coordination : bond 0.02132 / 1.31 ( 13) metal coordination : angle 15.47958 / 11.28 ( 39) Misc. bond : bond 0.13541 / 8.78 ( 41) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 619 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7888 (mptp) cc_final: 0.7231 (mtpp) REVERT: A 127 ASP cc_start: 0.7213 (t0) cc_final: 0.6835 (t0) REVERT: A 204 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7758 (tt0) REVERT: A 249 PHE cc_start: 0.8721 (m-80) cc_final: 0.8500 (m-80) REVERT: A 327 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6720 (mtt90) REVERT: A 364 MET cc_start: 0.8765 (tpp) cc_final: 0.8530 (tpp) REVERT: A 408 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7857 (mmmt) REVERT: A 423 LYS cc_start: 0.8090 (mttt) cc_final: 0.7765 (mttt) REVERT: A 471 PHE cc_start: 0.8749 (m-80) cc_final: 0.8271 (m-80) REVERT: A 514 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7004 (p0) REVERT: A 516 LEU cc_start: 0.8561 (mp) cc_final: 0.8314 (mt) REVERT: A 682 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: a 88 PHE cc_start: 0.8388 (m-10) cc_final: 0.7978 (m-10) REVERT: a 96 SER cc_start: 0.8102 (t) cc_final: 0.7566 (m) REVERT: a 151 PHE cc_start: 0.7402 (m-80) cc_final: 0.6935 (m-80) REVERT: a 168 ASN cc_start: 0.8658 (t0) cc_final: 0.8286 (t0) REVERT: a 182 ASP cc_start: 0.7485 (t0) cc_final: 0.6898 (p0) REVERT: a 253 PHE cc_start: 0.7655 (m-80) cc_final: 0.7440 (m-80) REVERT: a 266 ASN cc_start: 0.6256 (m-40) cc_final: 0.5944 (m110) REVERT: a 310 TYR cc_start: 0.8867 (m-80) cc_final: 0.7901 (m-80) REVERT: a 414 LYS cc_start: 0.8127 (mptt) cc_final: 0.7728 (mmmt) REVERT: a 418 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: a 469 PRO cc_start: 0.7955 (Cg_exo) cc_final: 0.7568 (Cg_endo) REVERT: a 472 GLN cc_start: 0.6813 (pm20) cc_final: 0.6442 (pm20) REVERT: a 560 TRP cc_start: 0.7840 (m-10) cc_final: 0.7354 (m100) REVERT: a 647 ARG cc_start: 0.7812 (mtt-85) cc_final: 0.7436 (mtt-85) REVERT: a 664 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7244 (mtp180) REVERT: B 164 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6751 (t70) REVERT: B 171 ARG cc_start: 0.8250 (mmt180) cc_final: 0.7905 (mmt90) REVERT: B 181 SER cc_start: 0.6845 (m) cc_final: 0.6533 (p) REVERT: C 50 MET cc_start: 0.7662 (mmp) cc_final: 0.7443 (mpp) REVERT: C 79 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7817 (mp) REVERT: C 102 LYS cc_start: 0.8478 (mtmt) cc_final: 0.7782 (mtpt) REVERT: c 69 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.5725 (tmm) REVERT: c 90 MET cc_start: 0.3769 (OUTLIER) cc_final: 0.3188 (mtp) REVERT: D 69 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7714 (mtp85) REVERT: E 25 GLU cc_start: 0.7222 (pp20) cc_final: 0.6759 (pp20) REVERT: U 29 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7826 (mtmm) REVERT: U 52 LYS cc_start: 0.8305 (mttt) cc_final: 0.7747 (mptt) REVERT: U 337 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7586 (tm-30) REVERT: V 67 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8671 (mt) REVERT: V 81 LYS cc_start: 0.8741 (tttt) cc_final: 0.7626 (mtmm) REVERT: V 168 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7522 (mmtm) REVERT: W 50 ASP cc_start: 0.7514 (m-30) cc_final: 0.6958 (m-30) REVERT: W 94 GLU cc_start: 0.7211 (mp0) cc_final: 0.6850 (mp0) REVERT: W 242 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8115 (mp) REVERT: W 253 GLN cc_start: 0.7940 (tt0) cc_final: 0.7719 (mt0) REVERT: X 95 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8014 (ttm-80) REVERT: X 99 VAL cc_start: 0.7771 (t) cc_final: 0.7398 (m) REVERT: X 193 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7774 (mm) REVERT: X 232 MET cc_start: 0.7875 (ttm) cc_final: 0.7607 (ttp) REVERT: X 347 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7683 (mtp180) REVERT: Y 52 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7715 (mttm) REVERT: Y 141 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: Y 198 GLN cc_start: 0.7771 (tt0) cc_final: 0.7351 (mt0) REVERT: Y 255 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7441 (mt-10) REVERT: Y 268 LYS cc_start: 0.7570 (tmmt) cc_final: 0.7204 (tttm) REVERT: Z 31 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8164 (mptt) REVERT: Z 52 LYS cc_start: 0.8430 (mttt) cc_final: 0.8121 (mtmt) REVERT: Z 68 SER cc_start: 0.8489 (m) cc_final: 0.8106 (t) REVERT: Z 140 MET cc_start: 0.8154 (tpp) cc_final: 0.7467 (tpp) REVERT: Z 194 ASN cc_start: 0.7437 (t0) cc_final: 0.6805 (m110) REVERT: Z 195 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: Z 272 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: Z 310 ASP cc_start: 0.7807 (t0) cc_final: 0.7580 (t0) outliers start: 135 outliers final: 90 residues processed: 703 average time/residue: 0.2474 time to fit residues: 282.7451 Evaluate side-chains 709 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 602 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 85 VAL Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 128 THR Chi-restraints excluded: chain a residue 157 LEU Chi-restraints excluded: chain a residue 213 MET Chi-restraints excluded: chain a residue 341 SER Chi-restraints excluded: chain a residue 355 LEU Chi-restraints excluded: chain a residue 358 SER Chi-restraints excluded: chain a residue 403 MET Chi-restraints excluded: chain a residue 418 GLN Chi-restraints excluded: chain a residue 465 LEU Chi-restraints excluded: chain a residue 509 THR Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 542 ASP Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 610 SER Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain a residue 700 THR Chi-restraints excluded: chain a residue 708 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain c residue 69 MET Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 105 SER Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 186 ILE Chi-restraints excluded: chain U residue 191 THR Chi-restraints excluded: chain U residue 198 GLN Chi-restraints excluded: chain U residue 209 ASN Chi-restraints excluded: chain U residue 221 SER Chi-restraints excluded: chain V residue 18 ILE Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 200 ILE Chi-restraints excluded: chain V residue 221 SER Chi-restraints excluded: chain V residue 277 SER Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 198 GLN Chi-restraints excluded: chain W residue 224 ARG Chi-restraints excluded: chain W residue 242 LEU Chi-restraints excluded: chain W residue 267 VAL Chi-restraints excluded: chain W residue 357 VAL Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 76 ASP Chi-restraints excluded: chain X residue 95 ARG Chi-restraints excluded: chain X residue 173 THR Chi-restraints excluded: chain X residue 193 LEU Chi-restraints excluded: chain X residue 253 GLN Chi-restraints excluded: chain X residue 262 SER Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 317 LEU Chi-restraints excluded: chain X residue 323 ILE Chi-restraints excluded: chain Y residue 103 MET Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 141 GLN Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain Z residue 54 ASN Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 104 VAL Chi-restraints excluded: chain Z residue 105 SER Chi-restraints excluded: chain Z residue 138 ILE Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 246 ASP Chi-restraints excluded: chain Z residue 272 GLU Chi-restraints excluded: chain Z residue 293 ILE Chi-restraints excluded: chain Z residue 335 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 251 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 312 optimal weight: 2.9990 chunk 347 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 377 optimal weight: 8.9990 chunk 325 optimal weight: 4.9990 chunk 206 optimal weight: 50.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 587 HIS U 90 ASN ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 209 ASN ** V 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 289 ASN ** W 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 HIS ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 312 GLN ** 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 = 0.3841 r_free = 0.3841 target = 0.168976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.151759 restraints weight = 46230.134| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.43 r_work: 0.3523 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.588 39144 Z= 0.167 Angle : 0.885 64.576 54136 Z= 0.326 Chirality : 0.044 0.312 5378 Planarity : 0.004 0.063 6624 Dihedral : 13.922 160.899 6839 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.50 % Favored : 95.45 % Rotamer: Outliers : 3.45 % Allowed : 20.86 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.13), residues: 3976 helix: 0.24 (0.13), residues: 1447 sheet: -0.88 (0.17), residues: 1005 loop : -1.38 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Z 224 TYR 0.026 0.002 TYR a 202 PHE 0.028 0.002 PHE a 686 TRP 0.031 0.001 TRP U 184 HIS 0.006 0.001 HIS W 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (39090) covalent geometry : angle 0.78260 / 0.32 (54097) hydrogen bonds : bond 0.04054 / 2.72 ( 1365) hydrogen bonds : angle 5.27259 / 3.90 ( 3972) metal coordination : bond 0.01655 / 1.01 ( 13) metal coordination : angle 15.43647 / 11.20 ( 39) Misc. bond : bond 0.13915 / 8.92 ( 41) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 611 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7876 (mptp) cc_final: 0.7272 (mtpp) REVERT: A 127 ASP cc_start: 0.7089 (t0) cc_final: 0.6716 (t0) REVERT: A 327 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.6681 (mtt90) REVERT: A 364 MET cc_start: 0.8743 (tpp) cc_final: 0.8537 (tpp) REVERT: A 408 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7802 (mmmt) REVERT: A 423 LYS cc_start: 0.8075 (mttt) cc_final: 0.7728 (mttt) REVERT: A 514 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7008 (p0) REVERT: A 516 LEU cc_start: 0.8491 (mp) cc_final: 0.8269 (mt) REVERT: A 682 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6940 (m-80) REVERT: a 88 PHE cc_start: 0.8387 (m-10) cc_final: 0.7991 (m-10) REVERT: a 96 SER cc_start: 0.8032 (t) cc_final: 0.7506 (m) REVERT: a 151 PHE cc_start: 0.7354 (m-80) cc_final: 0.6883 (m-80) REVERT: a 168 ASN cc_start: 0.8625 (t0) cc_final: 0.8267 (t0) REVERT: a 182 ASP cc_start: 0.7464 (t0) cc_final: 0.6957 (p0) REVERT: a 212 TYR cc_start: 0.8449 (t80) cc_final: 0.8172 (t80) REVERT: a 253 PHE cc_start: 0.7602 (m-80) cc_final: 0.7386 (m-80) REVERT: a 310 TYR cc_start: 0.8802 (m-80) cc_final: 0.7890 (m-80) REVERT: a 414 LYS cc_start: 0.7913 (mptt) cc_final: 0.7694 (mmmt) REVERT: a 469 PRO cc_start: 0.7961 (Cg_exo) cc_final: 0.7578 (Cg_endo) REVERT: a 472 GLN cc_start: 0.6818 (pm20) cc_final: 0.6499 (pm20) REVERT: a 528 LEU cc_start: 0.8695 (mt) cc_final: 0.8353 (mp) REVERT: a 647 ARG cc_start: 0.7754 (mtt-85) cc_final: 0.7459 (mtt-85) REVERT: a 664 ARG cc_start: 0.7935 (mtt90) cc_final: 0.7323 (mtp180) REVERT: B 164 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6562 (t70) REVERT: B 171 ARG cc_start: 0.8234 (mmt180) cc_final: 0.7997 (mmt90) REVERT: B 181 SER cc_start: 0.6889 (m) cc_final: 0.6585 (p) REVERT: C 79 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7875 (mp) REVERT: C 102 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7739 (mtpt) REVERT: c 24 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6867 (m-10) REVERT: c 69 MET cc_start: 0.6738 (tpt) cc_final: 0.5798 (tmm) REVERT: c 90 MET cc_start: 0.3824 (OUTLIER) cc_final: 0.3238 (mtp) REVERT: D 69 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7789 (mtp85) REVERT: U 29 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7762 (mtmm) REVERT: U 52 LYS cc_start: 0.8262 (mttt) cc_final: 0.7800 (mptt) REVERT: U 337 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7562 (tm-30) REVERT: V 81 LYS cc_start: 0.8731 (tttt) cc_final: 0.8422 (tptp) REVERT: V 159 LEU cc_start: 0.8479 (mt) cc_final: 0.8246 (mt) REVERT: V 160 ILE cc_start: 0.8443 (mt) cc_final: 0.8086 (pt) REVERT: V 168 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7569 (mmtm) REVERT: W 50 ASP cc_start: 0.7477 (m-30) cc_final: 0.6935 (m-30) REVERT: W 94 GLU cc_start: 0.7223 (mp0) cc_final: 0.6878 (mp0) REVERT: W 195 GLU cc_start: 0.7487 (tp30) cc_final: 0.7076 (tp30) REVERT: W 242 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8126 (mp) REVERT: W 253 GLN cc_start: 0.7847 (tt0) cc_final: 0.7620 (mt0) REVERT: X 95 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7692 (ttt90) REVERT: X 99 VAL cc_start: 0.7733 (t) cc_final: 0.7370 (m) REVERT: X 193 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7774 (mm) REVERT: X 232 MET cc_start: 0.7782 (ttm) cc_final: 0.7541 (ttp) REVERT: X 285 ARG cc_start: 0.7435 (mtp85) cc_final: 0.6988 (ttm-80) REVERT: X 347 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7657 (mtp180) REVERT: Y 52 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7781 (mttm) REVERT: Y 141 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: Y 198 GLN cc_start: 0.7722 (tt0) cc_final: 0.7327 (mt0) REVERT: Y 255 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7429 (mt-10) REVERT: Y 268 LYS cc_start: 0.7497 (tmmt) cc_final: 0.7212 (tttm) REVERT: Z 31 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8167 (mptt) REVERT: Z 52 LYS cc_start: 0.8446 (mttt) cc_final: 0.8137 (mtmt) REVERT: Z 140 MET cc_start: 0.8081 (tpp) cc_final: 0.7406 (tpp) REVERT: Z 194 ASN cc_start: 0.7450 (t0) cc_final: 0.6873 (m110) REVERT: Z 195 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: Z 255 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7083 (mm-30) REVERT: Z 272 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7123 (tp30) REVERT: Z 300 MET cc_start: 0.8330 (ptp) cc_final: 0.8058 (mtm) REVERT: Z 310 ASP cc_start: 0.7822 (t0) cc_final: 0.7588 (t0) outliers start: 115 outliers final: 82 residues processed: 681 average time/residue: 0.2351 time to fit residues: 260.7388 Evaluate side-chains 688 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 591 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 128 THR Chi-restraints excluded: chain a residue 157 LEU Chi-restraints excluded: chain a residue 341 SER Chi-restraints excluded: chain a residue 358 SER Chi-restraints excluded: chain a residue 403 MET Chi-restraints excluded: chain a residue 465 LEU Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 542 ASP Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 610 SER Chi-restraints excluded: chain a residue 688 LEU Chi-restraints excluded: chain a residue 692 PHE Chi-restraints excluded: chain a residue 700 THR Chi-restraints excluded: chain a residue 708 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain c residue 24 PHE Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 90 ASN Chi-restraints excluded: chain U residue 93 LYS Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 186 ILE Chi-restraints excluded: chain U residue 191 THR Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 221 SER Chi-restraints excluded: chain V residue 277 SER Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 48 ASP Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 242 LEU Chi-restraints excluded: chain W residue 267 VAL Chi-restraints excluded: chain W residue 357 VAL Chi-restraints excluded: chain X residue 11 THR Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 95 ARG Chi-restraints excluded: chain X residue 173 THR Chi-restraints excluded: chain X residue 193 LEU Chi-restraints excluded: chain X residue 253 GLN Chi-restraints excluded: chain X residue 262 SER Chi-restraints excluded: chain X residue 317 LEU Chi-restraints excluded: chain X residue 323 ILE Chi-restraints excluded: chain Y residue 103 MET Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 141 GLN Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain Z residue 54 ASN Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 104 VAL Chi-restraints excluded: chain Z residue 105 SER Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 246 ASP Chi-restraints excluded: chain Z residue 272 GLU Chi-restraints excluded: chain Z residue 293 ILE Chi-restraints excluded: chain Z residue 309 VAL Chi-restraints excluded: chain Z residue 335 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 15 optimal weight: 0.7980 chunk 152 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 204 optimal weight: 0.0970 chunk 255 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 ASN ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 209 ASN ** V 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 111 HIS ** W 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 198 GLN ** X 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 HIS ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 289 ASN ** Y 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 144 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.170071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.152032 restraints weight = 46549.813| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.52 r_work: 0.3519 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.572 39144 Z= 0.136 Angle : 0.857 63.494 54136 Z= 0.317 Chirality : 0.043 0.231 5378 Planarity : 0.004 0.060 6624 Dihedral : 13.649 156.442 6839 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 2.76 % Allowed : 21.86 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.99 (0.13), residues: 3976 helix: 0.34 (0.13), residues: 1460 sheet: -0.85 (0.17), residues: 1009 loop : -1.38 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG Z 224 TYR 0.027 0.001 TYR U 364 PHE 0.028 0.001 PHE a 254 TRP 0.028 0.001 TRP U 184 HIS 0.005 0.001 HIS X 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (39090) covalent geometry : angle 0.75448 / 0.31 (54097) hydrogen bonds : bond 0.03854 / 2.58 ( 1365) hydrogen bonds : angle 5.15545 / 3.82 ( 3972) metal coordination : bond 0.01415 / 0.87 ( 13) metal coordination : angle 15.18982 / 10.94 ( 39) Misc. bond : bond 0.14400 / 9.07 ( 41) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 627 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7860 (mptp) cc_final: 0.7289 (mtpp) REVERT: A 204 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7357 (tt0) REVERT: A 249 PHE cc_start: 0.8581 (m-80) cc_final: 0.8321 (m-80) REVERT: A 327 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.6467 (mtt90) REVERT: A 406 GLN cc_start: 0.7698 (mt0) cc_final: 0.7493 (mt0) REVERT: A 408 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7559 (mmmt) REVERT: A 423 LYS cc_start: 0.8131 (mttt) cc_final: 0.7790 (mttt) REVERT: A 471 PHE cc_start: 0.8718 (m-80) cc_final: 0.8229 (m-80) REVERT: A 514 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7029 (p0) REVERT: A 532 TYR cc_start: 0.8614 (m-80) cc_final: 0.8296 (m-80) REVERT: A 578 ASP cc_start: 0.7644 (m-30) cc_final: 0.7293 (m-30) REVERT: A 682 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6972 (m-80) REVERT: a 88 PHE cc_start: 0.8416 (m-10) cc_final: 0.8015 (m-10) REVERT: a 96 SER cc_start: 0.7983 (t) cc_final: 0.7458 (m) REVERT: a 151 PHE cc_start: 0.7426 (m-80) cc_final: 0.6932 (m-80) REVERT: a 168 ASN cc_start: 0.8406 (t0) cc_final: 0.8126 (t0) REVERT: a 182 ASP cc_start: 0.7482 (t0) cc_final: 0.6983 (p0) REVERT: a 212 TYR cc_start: 0.8374 (t80) cc_final: 0.8103 (t80) REVERT: a 235 ASP cc_start: 0.7520 (t0) cc_final: 0.6197 (m-30) REVERT: a 253 PHE cc_start: 0.7641 (m-80) cc_final: 0.7423 (m-80) REVERT: a 310 TYR cc_start: 0.8841 (m-80) cc_final: 0.7915 (m-80) REVERT: a 377 ILE cc_start: 0.8778 (mt) cc_final: 0.8560 (mm) REVERT: a 414 LYS cc_start: 0.7916 (mptt) cc_final: 0.7664 (mmmt) REVERT: a 469 PRO cc_start: 0.7887 (Cg_exo) cc_final: 0.7454 (Cg_endo) REVERT: a 472 GLN cc_start: 0.6773 (pm20) cc_final: 0.6474 (pm20) REVERT: a 528 LEU cc_start: 0.8639 (mt) cc_final: 0.8341 (mp) REVERT: a 647 ARG cc_start: 0.7796 (mtt-85) cc_final: 0.7519 (mtt-85) REVERT: a 655 LYS cc_start: 0.7808 (ttpp) cc_final: 0.7169 (tppt) REVERT: a 664 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7254 (mtp180) REVERT: B 164 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6535 (t70) REVERT: B 181 SER cc_start: 0.6812 (m) cc_final: 0.6556 (p) REVERT: C 79 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7833 (mp) REVERT: C 102 LYS cc_start: 0.8324 (mtmt) cc_final: 0.7715 (mtpt) REVERT: c 24 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6658 (m-10) REVERT: c 69 MET cc_start: 0.6715 (tpt) cc_final: 0.5709 (tmm) REVERT: c 90 MET cc_start: 0.3690 (OUTLIER) cc_final: 0.3079 (mtp) REVERT: U 29 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7811 (mtmm) REVERT: U 52 LYS cc_start: 0.8332 (mttt) cc_final: 0.7866 (mptt) REVERT: U 149 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8125 (tp) REVERT: U 312 GLN cc_start: 0.8572 (tt0) cc_final: 0.8151 (tp40) REVERT: U 337 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7696 (tm-30) REVERT: V 81 LYS cc_start: 0.8775 (tttt) cc_final: 0.8489 (tptp) REVERT: V 159 LEU cc_start: 0.8410 (mt) cc_final: 0.8156 (mt) REVERT: V 160 ILE cc_start: 0.8492 (mt) cc_final: 0.8092 (pt) REVERT: V 168 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7533 (mmtm) REVERT: V 322 LYS cc_start: 0.8289 (mttt) cc_final: 0.7717 (ptmt) REVERT: W 50 ASP cc_start: 0.7502 (m-30) cc_final: 0.6972 (m-30) REVERT: W 74 ILE cc_start: 0.8475 (mp) cc_final: 0.8136 (mm) REVERT: W 94 GLU cc_start: 0.7142 (mp0) cc_final: 0.6806 (mp0) REVERT: W 195 GLU cc_start: 0.7437 (tp30) cc_final: 0.6959 (tt0) REVERT: X 52 LYS cc_start: 0.7236 (mttp) cc_final: 0.6540 (ptmm) REVERT: X 71 PHE cc_start: 0.8440 (m-80) cc_final: 0.8058 (m-10) REVERT: X 95 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.7774 (ttt90) REVERT: X 99 VAL cc_start: 0.7672 (t) cc_final: 0.7345 (m) REVERT: X 193 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7736 (mm) REVERT: X 232 MET cc_start: 0.7734 (ttm) cc_final: 0.7468 (ttp) REVERT: X 347 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7759 (mtp180) REVERT: Y 52 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7771 (mttm) REVERT: Y 141 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: Y 198 GLN cc_start: 0.7634 (tt0) cc_final: 0.7283 (mt0) REVERT: Y 255 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7480 (mt-10) REVERT: Y 268 LYS cc_start: 0.7437 (tmmt) cc_final: 0.7167 (tttm) REVERT: Z 52 LYS cc_start: 0.8534 (mttt) cc_final: 0.8226 (mtmt) REVERT: Z 103 MET cc_start: 0.8379 (ppp) cc_final: 0.8152 (ppp) REVERT: Z 140 MET cc_start: 0.8111 (tpp) cc_final: 0.7627 (tpp) REVERT: Z 194 ASN cc_start: 0.7411 (t0) cc_final: 0.6876 (m110) REVERT: Z 195 GLU cc_start: 0.7790 (mp0) cc_final: 0.7483 (mp0) REVERT: Z 246 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7089 (m-30) REVERT: Z 255 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7000 (mm-30) REVERT: Z 272 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7148 (tp30) REVERT: Z 310 ASP cc_start: 0.7834 (t0) cc_final: 0.7602 (t0) REVERT: Z 339 ARG cc_start: 0.8131 (ttp-110) cc_final: 0.7891 (tmm160) outliers start: 92 outliers final: 61 residues processed: 683 average time/residue: 0.2335 time to fit residues: 257.6201 Evaluate side-chains 670 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 596 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 128 THR Chi-restraints excluded: chain a residue 157 LEU Chi-restraints excluded: chain a residue 341 SER Chi-restraints excluded: chain a residue 358 SER Chi-restraints excluded: chain a residue 465 LEU Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 542 ASP Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 610 SER Chi-restraints excluded: chain a residue 688 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain c residue 24 PHE Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 186 ILE Chi-restraints excluded: chain U residue 191 THR Chi-restraints excluded: chain U residue 255 GLU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 221 SER Chi-restraints excluded: chain V residue 277 SER Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 198 GLN Chi-restraints excluded: chain W residue 357 VAL Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 173 THR Chi-restraints excluded: chain X residue 193 LEU Chi-restraints excluded: chain X residue 253 GLN Chi-restraints excluded: chain X residue 262 SER Chi-restraints excluded: chain X residue 317 LEU Chi-restraints excluded: chain X residue 323 ILE Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 141 GLN Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 104 VAL Chi-restraints excluded: chain Z residue 105 SER Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 246 ASP Chi-restraints excluded: chain Z residue 272 GLU Chi-restraints excluded: chain Z residue 293 ILE Chi-restraints excluded: chain Z residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 146 optimal weight: 6.9990 chunk 167 optimal weight: 0.0970 chunk 266 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 365 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** U 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 289 ASN ** W 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 198 GLN X 111 HIS ** X 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 HIS ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.171683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.154618 restraints weight = 46296.796| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.43 r_work: 0.3537 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.567 39144 Z= 0.152 Angle : 0.867 63.187 54136 Z= 0.320 Chirality : 0.044 0.216 5378 Planarity : 0.004 0.062 6624 Dihedral : 13.540 154.079 6839 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % Rotamer: Outliers : 2.64 % Allowed : 22.79 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.92 (0.13), residues: 3976 helix: 0.37 (0.13), residues: 1454 sheet: -0.82 (0.17), residues: 1006 loop : -1.29 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Z 224 TYR 0.040 0.002 TYR a 202 PHE 0.033 0.002 PHE a 180 TRP 0.035 0.001 TRP U 184 HIS 0.005 0.001 HIS a 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (39090) covalent geometry : angle 0.76481 / 0.32 (54097) hydrogen bonds : bond 0.03914 / 2.62 ( 1365) hydrogen bonds : angle 5.13001 / 3.81 ( 3972) metal coordination : bond 0.01509 / 0.91 ( 13) metal coordination : angle 15.20323 / 10.89 ( 39) Misc. bond : bond 0.14038 / 8.92 ( 41) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 600 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7884 (mptp) cc_final: 0.7353 (mtpp) REVERT: A 204 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7358 (tt0) REVERT: A 327 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7525 (mtt90) REVERT: A 408 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7682 (mmmt) REVERT: A 423 LYS cc_start: 0.8141 (mttt) cc_final: 0.7799 (mttt) REVERT: A 471 PHE cc_start: 0.8690 (m-80) cc_final: 0.8245 (m-80) REVERT: A 514 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7048 (p0) REVERT: A 532 TYR cc_start: 0.8611 (m-80) cc_final: 0.8356 (m-80) REVERT: A 578 ASP cc_start: 0.7704 (m-30) cc_final: 0.7344 (m-30) REVERT: a 88 PHE cc_start: 0.8403 (m-10) cc_final: 0.7994 (m-10) REVERT: a 96 SER cc_start: 0.7971 (t) cc_final: 0.7444 (m) REVERT: a 151 PHE cc_start: 0.7403 (m-80) cc_final: 0.6883 (m-80) REVERT: a 168 ASN cc_start: 0.8443 (t0) cc_final: 0.8157 (t0) REVERT: a 182 ASP cc_start: 0.7517 (t0) cc_final: 0.7032 (p0) REVERT: a 212 TYR cc_start: 0.8402 (t80) cc_final: 0.8135 (t80) REVERT: a 235 ASP cc_start: 0.7006 (t0) cc_final: 0.6072 (m-30) REVERT: a 253 PHE cc_start: 0.7628 (m-80) cc_final: 0.7395 (m-80) REVERT: a 310 TYR cc_start: 0.8901 (m-80) cc_final: 0.7894 (m-80) REVERT: a 414 LYS cc_start: 0.7918 (mptt) cc_final: 0.7717 (mmmt) REVERT: a 469 PRO cc_start: 0.7870 (Cg_exo) cc_final: 0.7447 (Cg_endo) REVERT: a 472 GLN cc_start: 0.6925 (pm20) cc_final: 0.6614 (pm20) REVERT: a 528 LEU cc_start: 0.8640 (mt) cc_final: 0.8296 (mp) REVERT: a 647 ARG cc_start: 0.7820 (mtt-85) cc_final: 0.7543 (mtt-85) REVERT: a 655 LYS cc_start: 0.7763 (ttpp) cc_final: 0.7136 (tppt) REVERT: a 664 ARG cc_start: 0.7955 (mtt90) cc_final: 0.7347 (mtp180) REVERT: B 6 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7019 (mp0) REVERT: B 164 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6585 (t70) REVERT: B 171 ARG cc_start: 0.8439 (tpp-160) cc_final: 0.7800 (ttm170) REVERT: B 181 SER cc_start: 0.6834 (m) cc_final: 0.6617 (p) REVERT: C 50 MET cc_start: 0.7623 (mmp) cc_final: 0.7394 (mpp) REVERT: C 79 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7844 (mp) REVERT: C 102 LYS cc_start: 0.8345 (mtmt) cc_final: 0.7764 (mtpt) REVERT: c 24 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6662 (m-10) REVERT: c 69 MET cc_start: 0.6731 (tpt) cc_final: 0.5776 (tmm) REVERT: c 90 MET cc_start: 0.3733 (OUTLIER) cc_final: 0.3122 (mtp) REVERT: U 29 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7823 (mtmm) REVERT: U 52 LYS cc_start: 0.8313 (mttt) cc_final: 0.7861 (mptt) REVERT: U 312 GLN cc_start: 0.8542 (tt0) cc_final: 0.8139 (tp40) REVERT: U 337 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7680 (tm-30) REVERT: V 81 LYS cc_start: 0.8793 (tttt) cc_final: 0.8524 (tptp) REVERT: V 159 LEU cc_start: 0.8455 (mt) cc_final: 0.8217 (mt) REVERT: V 168 LYS cc_start: 0.7870 (mtpt) cc_final: 0.7558 (mmtm) REVERT: V 322 LYS cc_start: 0.8290 (mttt) cc_final: 0.7738 (ptmt) REVERT: W 50 ASP cc_start: 0.7518 (m-30) cc_final: 0.6979 (m-30) REVERT: W 74 ILE cc_start: 0.8503 (mp) cc_final: 0.7979 (mt) REVERT: W 94 GLU cc_start: 0.7156 (mp0) cc_final: 0.6828 (mp0) REVERT: W 195 GLU cc_start: 0.7365 (tp30) cc_final: 0.6986 (tt0) REVERT: W 206 ASN cc_start: 0.5932 (m110) cc_final: 0.5652 (m-40) REVERT: W 325 TYR cc_start: 0.7929 (t80) cc_final: 0.7555 (t80) REVERT: X 71 PHE cc_start: 0.8443 (m-80) cc_final: 0.8080 (m-10) REVERT: X 95 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.7762 (ttt90) REVERT: X 99 VAL cc_start: 0.7687 (t) cc_final: 0.7371 (m) REVERT: X 149 LEU cc_start: 0.7585 (tt) cc_final: 0.7232 (tp) REVERT: X 193 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7777 (mm) REVERT: X 232 MET cc_start: 0.7752 (ttm) cc_final: 0.7464 (ttp) REVERT: X 347 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7806 (mtp180) REVERT: Y 52 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7835 (mttm) REVERT: Y 140 MET cc_start: 0.7143 (mmm) cc_final: 0.5729 (mtp) REVERT: Y 141 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: Y 255 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7531 (mt-10) REVERT: Y 268 LYS cc_start: 0.7390 (tmmt) cc_final: 0.7189 (tttm) REVERT: Z 52 LYS cc_start: 0.8531 (mttt) cc_final: 0.8243 (mtmt) REVERT: Z 140 MET cc_start: 0.8071 (tpp) cc_final: 0.7579 (tpp) REVERT: Z 194 ASN cc_start: 0.7411 (t0) cc_final: 0.6928 (m110) REVERT: Z 195 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: Z 246 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7087 (m-30) REVERT: Z 255 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7037 (mm-30) REVERT: Z 272 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7166 (tp30) REVERT: Z 310 ASP cc_start: 0.7862 (t0) cc_final: 0.7643 (t0) REVERT: Z 339 ARG cc_start: 0.8106 (ttp-110) cc_final: 0.7879 (tmm160) outliers start: 88 outliers final: 66 residues processed: 652 average time/residue: 0.2283 time to fit residues: 241.7799 Evaluate side-chains 666 residues out of total 3331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 588 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 TRP Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 692 PHE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain a residue 128 THR Chi-restraints excluded: chain a residue 135 ASP Chi-restraints excluded: chain a residue 157 LEU Chi-restraints excluded: chain a residue 341 SER Chi-restraints excluded: chain a residue 358 SER Chi-restraints excluded: chain a residue 465 LEU Chi-restraints excluded: chain a residue 538 VAL Chi-restraints excluded: chain a residue 542 ASP Chi-restraints excluded: chain a residue 559 CYS Chi-restraints excluded: chain a residue 610 SER Chi-restraints excluded: chain a residue 688 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain c residue 24 PHE Chi-restraints excluded: chain c residue 90 MET Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain U residue 77 SER Chi-restraints excluded: chain U residue 112 THR Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 186 ILE Chi-restraints excluded: chain U residue 191 THR Chi-restraints excluded: chain U residue 255 GLU Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 221 SER Chi-restraints excluded: chain V residue 277 SER Chi-restraints excluded: chain V residue 341 SER Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 198 GLN Chi-restraints excluded: chain W residue 357 VAL Chi-restraints excluded: chain X residue 36 VAL Chi-restraints excluded: chain X residue 50 ASP Chi-restraints excluded: chain X residue 173 THR Chi-restraints excluded: chain X residue 193 LEU Chi-restraints excluded: chain X residue 253 GLN Chi-restraints excluded: chain X residue 262 SER Chi-restraints excluded: chain X residue 323 ILE Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 141 GLN Chi-restraints excluded: chain Y residue 149 LEU Chi-restraints excluded: chain Z residue 10 THR Chi-restraints excluded: chain Z residue 14 SER Chi-restraints excluded: chain Z residue 54 ASN Chi-restraints excluded: chain Z residue 104 VAL Chi-restraints excluded: chain Z residue 105 SER Chi-restraints excluded: chain Z residue 167 VAL Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 205 VAL Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 246 ASP Chi-restraints excluded: chain Z residue 272 GLU Chi-restraints excluded: chain Z residue 293 ILE Chi-restraints excluded: chain Z residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 280 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 226 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 378 optimal weight: 0.8980 chunk 323 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 302 GLN ** a 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 209 ASN U 305 ASN ** V 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 253 GLN ** W 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 198 GLN ** X 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 HIS ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 312 GLN ** 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 = 0.3852 r_free = 0.3852 target = 0.170252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.153786 restraints weight = 46509.560| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.33 r_work: 0.3512 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.558 39144 Z= 0.175 Angle : 0.880 64.406 54136 Z= 0.325 Chirality : 0.044 0.207 5378 Planarity : 0.004 0.062 6624 Dihedral : 13.517 152.900 6839 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 2.76 % Allowed : 22.82 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.13), residues: 3976 helix: 0.35 (0.13), residues: 1455 sheet: -0.80 (0.17), residues: 1005 loop : -1.30 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Z 224 TYR 0.038 0.002 TYR a 202 PHE 0.029 0.002 PHE a 180 TRP 0.034 0.001 TRP U 184 HIS 0.006 0.001 HIS W 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (39090) covalent geometry : angle 0.77734 / 0.32 (54097) hydrogen bonds : bond 0.03959 / 2.65 ( 1365) hydrogen bonds : angle 5.14730 / 3.81 ( 3972) metal coordination : bond 0.01681 / 1.02 ( 13) metal coordination : angle 15.37486 / 11.02 ( 39) Misc. bond : bond 0.13690 / 8.76 ( 41) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11369.17 seconds wall clock time: 195 minutes 12.89 seconds (11712.89 seconds total)