Starting phenix.real_space_refine on Thu Sep 18 14:32:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5of4_3802/09_2025/5of4_3802.cif Found real_map, /net/cci-nas-00/data/ceres_data/5of4_3802/09_2025/5of4_3802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5of4_3802/09_2025/5of4_3802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5of4_3802/09_2025/5of4_3802.map" model { file = "/net/cci-nas-00/data/ceres_data/5of4_3802/09_2025/5of4_3802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5of4_3802/09_2025/5of4_3802.cif" } resolution = 4.4 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= 0.004 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 81 5.16 5 C 10827 2.51 5 N 3081 2.21 5 O 3207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17200 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3887 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 15, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 36, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 5671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5671 Classifications: {'peptide': 724} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 691} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 2, 'ARG:plan': 6, 'GLN:plan1': 3, 'HIS:plan': 3, 'ASP:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "D" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 5, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1451 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "F" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1498 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "G" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "H" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 620 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'TRANS': 123} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 124 Planarities with less than four sites: {'UNK:plan-1': 124} Unresolved non-hydrogen planarities: 124 Chain: "Z" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1350 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 270} Link IDs: {'TRANS': 269} Chain breaks: 15 Unresolved non-hydrogen bonds: 540 Unresolved non-hydrogen angles: 810 Unresolved non-hydrogen dihedrals: 270 Planarities with less than four sites: {'UNK:plan-1': 270} Unresolved non-hydrogen planarities: 270 Chain: "Y" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1160 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 232} Link IDs: {'TRANS': 231} Chain breaks: 18 Unresolved non-hydrogen bonds: 464 Unresolved non-hydrogen angles: 696 Unresolved non-hydrogen dihedrals: 232 Planarities with less than four sites: {'UNK:plan-1': 232} Unresolved non-hydrogen planarities: 232 Chain: "X" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 390 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'CIS': 1, 'TRANS': 76} Chain breaks: 6 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'UNK:plan-1': 78} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4744 SG CYS B 116 30.474 85.833 90.763 1.00110.23 S ATOM 5001 SG CYS B 155 26.916 88.074 96.067 1.00314.68 S ATOM 4884 SG CYS B 134 30.325 91.193 92.387 1.00147.22 S ATOM 5290 SG CYS B 190 32.215 86.707 97.680 1.00100.13 S Time building chain proxies: 3.39, per 1000 atoms: 0.20 Number of scatterers: 17200 At special positions: 0 Unit cell: (163.68, 158.4, 129.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 81 16.00 O 3207 8.00 N 3081 7.00 C 10827 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=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 511.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " Number of angles added : 12 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4766 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 12 sheets defined 79.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 242 through 256 removed outlier: 4.008A pdb=" N UNK A 246 " --> pdb=" O UNK A 242 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N UNK A 247 " --> pdb=" O UNK A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 317 through 329 removed outlier: 3.550A pdb=" N GLU A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 358 removed outlier: 3.577A pdb=" N ARG A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.605A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 425 " --> pdb=" O TRP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 492 through 498 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.914A pdb=" N TYR A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 536 Processing helix chain 'A' and resid 537 through 554 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 585 through 598 Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 667 through 684 removed outlier: 3.953A pdb=" N LYS A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 699 Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.579A pdb=" N GLN A 709 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 removed outlier: 3.876A pdb=" N ASP A 723 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 removed outlier: 4.347A pdb=" N ARG B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 61 Processing helix chain 'B' and resid 76 through 99 removed outlier: 3.872A pdb=" N GLU B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 Processing helix chain 'B' and resid 155 through 167 removed outlier: 3.771A pdb=" N GLU B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.808A pdb=" N LEU B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 209 through 213 removed outlier: 3.511A pdb=" N LEU B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 209 through 213' Processing helix chain 'B' and resid 238 through 248 Processing helix chain 'B' and resid 253 through 272 Processing helix chain 'B' and resid 275 through 291 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 324 through 347 removed outlier: 3.840A pdb=" N HIS B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 365 removed outlier: 4.400A pdb=" N LEU B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 385 removed outlier: 5.689A pdb=" N ALA B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 410 Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 440 through 451 Proline residue: B 446 - end of helix removed outlier: 3.824A pdb=" N PHE B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 removed outlier: 3.793A pdb=" N LYS B 469 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 531 Processing helix chain 'B' and resid 541 through 555 Processing helix chain 'B' and resid 558 through 565 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 604 through 609 removed outlier: 4.360A pdb=" N ILE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 604 through 609' Processing helix chain 'B' and resid 630 through 642 Processing helix chain 'B' and resid 646 through 665 removed outlier: 4.043A pdb=" N ASP B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 700 Processing helix chain 'B' and resid 709 through 726 Processing helix chain 'D' and resid 386 through 397 Processing helix chain 'D' and resid 415 through 428 Processing helix chain 'D' and resid 447 through 458 removed outlier: 4.482A pdb=" N ARG D 453 " --> pdb=" O SER D 449 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN D 458 " --> pdb=" O PHE D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 79 through 99 removed outlier: 3.708A pdb=" N CYS E 83 " --> pdb=" O ASN E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 134 removed outlier: 3.883A pdb=" N HIS E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 144 through 158 removed outlier: 3.930A pdb=" N SER E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N HIS E 158 " --> pdb=" O GLN E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 193 removed outlier: 3.741A pdb=" N LYS E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 224 through 237 removed outlier: 3.943A pdb=" N SER E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 25 Processing helix chain 'F' and resid 33 through 52 removed outlier: 4.034A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 121 Processing helix chain 'F' and resid 130 through 151 removed outlier: 3.776A pdb=" N VAL F 151 " --> pdb=" O MET F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.544A pdb=" N PHE F 177 " --> pdb=" O GLN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 211 removed outlier: 3.768A pdb=" N GLN F 204 " --> pdb=" O SER F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 232 Processing helix chain 'G' and resid 13 through 25 Processing helix chain 'G' and resid 57 through 67 removed outlier: 5.530A pdb=" N GLN G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 60 removed outlier: 3.757A pdb=" N UNK H 51 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N UNK H 60 " --> pdb=" O UNK H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 71 removed outlier: 3.703A pdb=" N UNK H 71 " --> pdb=" O UNK H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 88 Processing helix chain 'H' and resid 94 through 103 Processing helix chain 'H' and resid 107 through 168 Processing helix chain 'Z' and resid 103 through 118 removed outlier: 3.615A pdb=" N UNK Z 116 " --> pdb=" O UNK Z 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 172 through 180 Processing helix chain 'Z' and resid 209 through 223 Processing helix chain 'Z' and resid 251 through 267 Processing helix chain 'Z' and resid 282 through 293 Processing helix chain 'Z' and resid 402 through 421 Processing helix chain 'Z' and resid 431 through 454 Processing helix chain 'Z' and resid 466 through 487 Processing helix chain 'Z' and resid 502 through 519 Processing helix chain 'Z' and resid 533 through 538 Processing helix chain 'Z' and resid 552 through 559 Processing helix chain 'Z' and resid 572 through 583 Processing helix chain 'Y' and resid 37 through 49 Processing helix chain 'Y' and resid 62 through 74 Processing helix chain 'Y' and resid 105 through 105 No H-bonds generated for 'chain 'Y' and resid 105 through 105' Processing helix chain 'Y' and resid 108 through 117 Processing helix chain 'Y' and resid 122 through 130 removed outlier: 4.434A pdb=" N UNK Y 130 " --> pdb=" O UNK Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 146 Processing helix chain 'Y' and resid 237 through 249 Processing helix chain 'Y' and resid 262 through 271 Processing helix chain 'Y' and resid 304 through 320 Processing helix chain 'Y' and resid 374 through 383 Processing helix chain 'Y' and resid 500 through 511 Processing helix chain 'Y' and resid 602 through 612 removed outlier: 3.822A pdb=" N UNK Y 612 " --> pdb=" O UNK Y 608 " (cutoff:3.500A) Processing helix chain 'Y' and resid 645 through 649 removed outlier: 4.190A pdb=" N UNK Y 649 " --> pdb=" O UNK Y 646 " (cutoff:3.500A) Processing helix chain 'Y' and resid 663 through 670 Processing helix chain 'Y' and resid 688 through 698 Processing helix chain 'X' and resid 81 through 92 Processing helix chain 'X' and resid 135 through 144 Processing helix chain 'X' and resid 150 through 157 removed outlier: 3.809A pdb=" N UNK X 157 " --> pdb=" O UNK X 153 " (cutoff:3.500A) Processing helix chain 'X' and resid 738 through 750 Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 226 removed outlier: 6.756A pdb=" N UNK A 224 " --> pdb=" O ALA A 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 338 removed outlier: 5.661A pdb=" N MET A 438 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 466 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU A 440 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS A 361 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER A 408 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL A 363 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 512 removed outlier: 7.258A pdb=" N GLN A 506 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N SER A 661 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA A 508 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A 663 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 510 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 623 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 662 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLN A 625 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N SER A 664 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 204 through 208 Processing sheet with id=AA6, first strand: chain 'B' and resid 249 through 252 removed outlier: 3.662A pdb=" N SER B 436 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN B 351 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 492 through 494 removed outlier: 6.636A pdb=" N MET B 493 " --> pdb=" O PHE B 679 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL B 618 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA B 680 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET B 620 " --> pdb=" O ALA B 680 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B 536 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 402 through 405 Processing sheet with id=AA9, first strand: chain 'D' and resid 407 through 409 removed outlier: 6.067A pdb=" N VAL D 442 " --> pdb=" O VAL D 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 114 through 116 removed outlier: 6.795A pdb=" N LEU E 61 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE E 107 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL E 63 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR E 109 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL E 65 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE E 169 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL E 198 " --> pdb=" O HIS E 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 68 through 70 removed outlier: 4.097A pdb=" N ARG F 68 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA F 61 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASN F 9 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ALA F 58 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU F 11 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE F 60 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE F 13 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU F 10 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU F 162 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL F 12 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE F 164 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL F 14 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'X' and resid 162 through 163 973 hydrogen bonds defined for protein. 2859 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: 2.78 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.30: 2977 1.30 - 1.55: 13125 1.55 - 1.80: 1220 1.80 - 2.04: 83 2.04 - 2.29: 12 Bond restraints: 17417 Sorted by residual: bond pdb=" C TYR A 489 " pdb=" O TYR A 489 " ideal model delta sigma weight residual 1.236 1.051 0.185 1.20e-02 6.94e+03 2.38e+02 bond pdb=" N PHE B 539 " pdb=" CA PHE B 539 " ideal model delta sigma weight residual 1.455 1.315 0.140 1.36e-02 5.41e+03 1.05e+02 bond pdb=" C PHE A 270 " pdb=" O PHE A 270 " ideal model delta sigma weight residual 1.236 1.340 -0.104 1.14e-02 7.69e+03 8.26e+01 bond pdb=" C UNK Y 245 " pdb=" O UNK Y 245 " ideal model delta sigma weight residual 1.232 1.409 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" C LEU A 464 " pdb=" O LEU A 464 " ideal model delta sigma weight residual 1.235 1.130 0.106 1.24e-02 6.50e+03 7.25e+01 ... (remaining 17412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.23: 23291 6.23 - 12.47: 370 12.47 - 18.70: 27 18.70 - 24.93: 1 24.93 - 31.16: 3 Bond angle restraints: 23692 Sorted by residual: angle pdb="FE1 SF4 B1000 " pdb=" S2 SF4 B1000 " pdb="FE4 SF4 B1000 " ideal model delta sigma weight residual 73.70 104.86 -31.16 1.50e+00 4.44e-01 4.32e+02 angle pdb=" S2 SF4 B1000 " pdb="FE4 SF4 B1000 " pdb=" S3 SF4 B1000 " ideal model delta sigma weight residual 104.10 75.24 28.86 1.50e+00 4.44e-01 3.70e+02 angle pdb=" S2 SF4 B1000 " pdb="FE1 SF4 B1000 " pdb=" S3 SF4 B1000 " ideal model delta sigma weight residual 104.10 76.60 27.50 1.50e+00 4.44e-01 3.36e+02 angle pdb="FE1 SF4 B1000 " pdb=" S3 SF4 B1000 " pdb="FE4 SF4 B1000 " ideal model delta sigma weight residual 73.70 98.08 -24.38 1.50e+00 4.44e-01 2.64e+02 angle pdb="FE2 SF4 B1000 " pdb=" S1 SF4 B1000 " pdb="FE3 SF4 B1000 " ideal model delta sigma weight residual 73.70 89.57 -15.87 1.50e+00 4.44e-01 1.12e+02 ... (remaining 23687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.35: 9396 14.35 - 28.70: 902 28.70 - 43.06: 192 43.06 - 57.41: 31 57.41 - 71.76: 4 Dihedral angle restraints: 10525 sinusoidal: 3287 harmonic: 7238 Sorted by residual: dihedral pdb=" CA PRO B 727 " pdb=" C PRO B 727 " pdb=" N PHE B 728 " pdb=" CA PHE B 728 " ideal model delta harmonic sigma weight residual 180.00 121.18 58.82 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA UNK D 378 " pdb=" C UNK D 378 " pdb=" N UNK D 379 " pdb=" CA UNK D 379 " ideal model delta harmonic sigma weight residual -180.00 -130.23 -49.77 0 5.00e+00 4.00e-02 9.91e+01 dihedral pdb=" CA UNK Z 88 " pdb=" C UNK Z 88 " pdb=" N UNK Z 89 " pdb=" CA UNK Z 89 " ideal model delta harmonic sigma weight residual -180.00 -130.78 -49.22 0 5.00e+00 4.00e-02 9.69e+01 ... (remaining 10522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 2823 0.305 - 0.610: 51 0.610 - 0.915: 3 0.915 - 1.220: 1 1.220 - 1.525: 1 Chirality restraints: 2879 Sorted by residual: chirality pdb="FE1 SF4 B1000 " pdb=" S2 SF4 B1000 " pdb=" S3 SF4 B1000 " pdb=" S4 SF4 B1000 " both_signs ideal model delta sigma weight residual False -10.55 -9.03 -1.53 2.00e-01 2.50e+01 5.82e+01 chirality pdb="FE4 SF4 B1000 " pdb=" S1 SF4 B1000 " pdb=" S2 SF4 B1000 " pdb=" S3 SF4 B1000 " both_signs ideal model delta sigma weight residual False 10.55 9.39 1.16 2.00e-01 2.50e+01 3.36e+01 chirality pdb=" CA UNK Y 512 " pdb=" N UNK Y 512 " pdb=" C UNK Y 512 " pdb=" CB UNK Y 512 " both_signs ideal model delta sigma weight residual False 2.52 1.80 0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 2876 not shown) Planarity restraints: 3082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 394 " 0.091 2.00e-02 2.50e+03 5.55e-02 7.71e+01 pdb=" CG TRP D 394 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 TRP D 394 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP D 394 " -0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP D 394 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP D 394 " -0.020 2.00e-02 2.50e+03 pdb=" CE3 TRP D 394 " -0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 394 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 394 " 0.053 2.00e-02 2.50e+03 pdb=" CH2 TRP D 394 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 319 " -0.056 2.00e-02 2.50e+03 5.12e-02 5.24e+01 pdb=" CG TYR A 319 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR A 319 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR A 319 " 0.089 2.00e-02 2.50e+03 pdb=" CE1 TYR A 319 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 319 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 319 " -0.083 2.00e-02 2.50e+03 pdb=" OH TYR A 319 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 482 " 0.079 2.00e-02 2.50e+03 4.91e-02 4.21e+01 pdb=" CG PHE A 482 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 482 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE A 482 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE A 482 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 PHE A 482 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 482 " 0.025 2.00e-02 2.50e+03 ... (remaining 3079 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 84 2.55 - 3.14: 12717 3.14 - 3.72: 26282 3.72 - 4.31: 34269 4.31 - 4.90: 54706 Nonbonded interactions: 128058 Sorted by model distance: nonbonded pdb=" O UNK Y 698 " pdb=" O UNK Y 699 " model vdw 1.962 3.040 nonbonded pdb=" O UNK X 752 " pdb=" CB UNK X 752 " model vdw 2.185 2.752 nonbonded pdb=" OE1 GLN A 668 " pdb=" O ASN G 64 " model vdw 2.243 3.040 nonbonded pdb=" O ILE A 531 " pdb=" OG1 THR A 535 " model vdw 2.248 3.040 nonbonded pdb=" NH2 ARG B 61 " pdb=" O PRO B 103 " model vdw 2.255 3.120 ... (remaining 128053 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 'Y' selection = (chain 'Z' and resid 110 through 584) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.400 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 : 0.022 0.208 17421 Z= 1.283 Angle : 2.193 43.976 23704 Z= 1.227 Chirality : 0.124 1.525 2879 Planarity : 0.011 0.116 3082 Dihedral : 12.454 71.759 5759 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.71 % Allowed : 11.46 % Favored : 87.84 % Rotamer: Outliers : 1.90 % Allowed : 4.29 % Favored : 93.81 % Cbeta Deviations : 0.80 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.97 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.34 (0.16), residues: 1702 helix: -2.08 (0.15), residues: 767 sheet: -2.69 (0.30), residues: 232 loop : -3.82 (0.19), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.004 ARG D 400 TYR 0.089 0.015 TYR A 319 PHE 0.079 0.013 PHE A 482 TRP 0.091 0.019 TRP D 394 HIS 0.031 0.007 HIS F 145 Details of bonding type rmsd covalent geometry : bond 0.02153 (17417) covalent geometry : angle 2.14965 (23692) hydrogen bonds : bond 0.12940 ( 973) hydrogen bonds : angle 7.80432 ( 2859) metal coordination : bond 0.05337 ( 4) metal coordination : angle 19.44684 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 521 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 284 CYS cc_start: 0.9409 (m) cc_final: 0.9096 (t) REVERT: A 294 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8499 (tm-30) REVERT: A 309 ASP cc_start: 0.5806 (m-30) cc_final: 0.4747 (m-30) REVERT: A 315 VAL cc_start: 0.8340 (t) cc_final: 0.8090 (p) REVERT: A 322 LYS cc_start: 0.8720 (tttt) cc_final: 0.8355 (mmtm) REVERT: A 340 LEU cc_start: 0.8885 (mt) cc_final: 0.8430 (mt) REVERT: A 452 ARG cc_start: 0.9317 (mtt180) cc_final: 0.9031 (tmm-80) REVERT: A 464 LEU cc_start: 0.9638 (tp) cc_final: 0.9394 (tp) REVERT: A 495 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8830 (tp30) REVERT: A 501 TYR cc_start: 0.9281 (p90) cc_final: 0.9002 (p90) REVERT: A 536 MET cc_start: 0.9069 (mtp) cc_final: 0.8773 (mtp) REVERT: A 553 ARG cc_start: 0.8577 (mmt90) cc_final: 0.8265 (mmt-90) REVERT: A 605 ILE cc_start: 0.9392 (tt) cc_final: 0.8966 (mt) REVERT: A 633 ARG cc_start: 0.8888 (mpp-170) cc_final: 0.8612 (mmm-85) REVERT: A 650 MET cc_start: 0.6299 (ttp) cc_final: 0.5897 (ttt) REVERT: A 674 THR cc_start: 0.9061 (m) cc_final: 0.8773 (p) REVERT: A 698 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8802 (pt0) REVERT: B 57 MET cc_start: 0.9562 (mtp) cc_final: 0.9199 (tpp) REVERT: B 88 ARG cc_start: 0.9180 (mmm160) cc_final: 0.8753 (mtp85) REVERT: B 105 LEU cc_start: 0.9331 (tp) cc_final: 0.8958 (tp) REVERT: B 174 ILE cc_start: 0.8984 (tt) cc_final: 0.8402 (tt) REVERT: B 227 ARG cc_start: 0.8769 (mtt180) cc_final: 0.8396 (mtm-85) REVERT: B 233 PHE cc_start: 0.9312 (m-80) cc_final: 0.9026 (m-80) REVERT: B 368 GLN cc_start: 0.9258 (mt0) cc_final: 0.9023 (pm20) REVERT: B 380 ARG cc_start: 0.9499 (tpt170) cc_final: 0.9242 (ppt170) REVERT: B 393 ASP cc_start: 0.9654 (m-30) cc_final: 0.9331 (t0) REVERT: B 419 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8815 (tm-30) REVERT: B 454 VAL cc_start: 0.9097 (m) cc_final: 0.8749 (p) REVERT: B 493 MET cc_start: 0.9310 (ttp) cc_final: 0.9046 (tmm) REVERT: B 504 ILE cc_start: 0.8477 (mt) cc_final: 0.8186 (tt) REVERT: B 526 GLU cc_start: 0.9508 (mt-10) cc_final: 0.8231 (mt-10) REVERT: B 618 VAL cc_start: 0.7744 (t) cc_final: 0.7514 (t) REVERT: B 641 ARG cc_start: 0.9198 (tmt90) cc_final: 0.8928 (tmm-80) REVERT: D 404 THR cc_start: 0.9098 (m) cc_final: 0.8763 (p) REVERT: D 405 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8096 (tp30) REVERT: D 426 ARG cc_start: 0.9012 (ttt180) cc_final: 0.8795 (ptm160) REVERT: D 433 PHE cc_start: 0.9239 (t80) cc_final: 0.8763 (t80) REVERT: D 434 GLU cc_start: 0.9062 (pp20) cc_final: 0.8690 (tp30) REVERT: E 63 VAL cc_start: 0.9396 (t) cc_final: 0.9196 (m) REVERT: E 79 ASN cc_start: 0.8806 (m-40) cc_final: 0.8492 (m-40) REVERT: E 94 GLU cc_start: 0.9366 (tt0) cc_final: 0.9058 (tp30) REVERT: E 98 GLN cc_start: 0.9032 (mm110) cc_final: 0.8783 (tp40) REVERT: E 103 GLN cc_start: 0.9417 (pt0) cc_final: 0.9012 (pt0) REVERT: E 112 LYS cc_start: 0.7740 (mttt) cc_final: 0.7326 (tttm) REVERT: E 123 ASN cc_start: 0.9535 (m-40) cc_final: 0.8995 (p0) REVERT: E 137 MET cc_start: 0.8820 (ttm) cc_final: 0.8386 (ttm) REVERT: E 166 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8436 (mm-30) REVERT: E 167 VAL cc_start: 0.9245 (t) cc_final: 0.9017 (p) REVERT: E 171 PHE cc_start: 0.8785 (t80) cc_final: 0.8369 (t80) REVERT: E 178 ASP cc_start: 0.8353 (p0) cc_final: 0.7804 (p0) REVERT: E 204 GLU cc_start: 0.8390 (tt0) cc_final: 0.7979 (tm-30) REVERT: E 214 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8300 (tp30) REVERT: E 221 VAL cc_start: 0.9297 (t) cc_final: 0.8962 (p) REVERT: F 7 GLU cc_start: 0.8743 (tt0) cc_final: 0.8368 (mp0) REVERT: F 15 VAL cc_start: 0.9315 (t) cc_final: 0.9058 (p) REVERT: F 139 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7441 (tptt) REVERT: F 143 TYR cc_start: 0.9026 (t80) cc_final: 0.8809 (t80) REVERT: F 147 MET cc_start: 0.9342 (mmm) cc_final: 0.8803 (mmm) REVERT: F 160 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7780 (ttm110) REVERT: F 169 ASP cc_start: 0.8187 (t0) cc_final: 0.7859 (p0) REVERT: G 36 GLN cc_start: 0.9266 (tt0) cc_final: 0.8658 (tm-30) REVERT: G 56 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7837 (mmm160) outliers start: 27 outliers final: 6 residues processed: 540 average time/residue: 0.1391 time to fit residues: 107.0038 Evaluate side-chains 349 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 343 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN A 598 HIS ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN A 629 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 114 ASN B 164 HIS B 237 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 154 GLN F 48 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.095170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.080502 restraints weight = 83259.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.081946 restraints weight = 61635.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.083049 restraints weight = 48552.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.083891 restraints weight = 40142.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.084478 restraints weight = 34407.486| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17421 Z= 0.157 Angle : 0.889 56.050 23704 Z= 0.390 Chirality : 0.044 0.199 2879 Planarity : 0.005 0.076 3082 Dihedral : 6.635 40.078 2571 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.21 % Allowed : 4.85 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.18), residues: 1702 helix: -0.70 (0.17), residues: 782 sheet: -2.40 (0.31), residues: 244 loop : -3.56 (0.19), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 574 TYR 0.027 0.002 TYR B 14 PHE 0.025 0.002 PHE F 50 TRP 0.019 0.002 TRP D 394 HIS 0.010 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00330 (17417) covalent geometry : angle 0.76360 (23692) hydrogen bonds : bond 0.04307 ( 973) hydrogen bonds : angle 5.48200 ( 2859) metal coordination : bond 0.01362 ( 4) metal coordination : angle 20.22194 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 458 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.8199 (tttt) cc_final: 0.7813 (mmtm) REVERT: A 326 LYS cc_start: 0.7476 (tppt) cc_final: 0.6702 (ttpt) REVERT: A 340 LEU cc_start: 0.8463 (mt) cc_final: 0.8189 (mt) REVERT: A 373 GLN cc_start: 0.9007 (pt0) cc_final: 0.8770 (pt0) REVERT: A 450 MET cc_start: 0.8574 (tpt) cc_final: 0.8366 (mmm) REVERT: A 495 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8552 (tp30) REVERT: A 501 TYR cc_start: 0.8334 (p90) cc_final: 0.7825 (p90) REVERT: A 536 MET cc_start: 0.8213 (mtp) cc_final: 0.7691 (mtp) REVERT: A 636 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8360 (mt-10) REVERT: A 650 MET cc_start: 0.6576 (ttp) cc_final: 0.6271 (ttt) REVERT: B 56 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9092 (mt) REVERT: B 76 THR cc_start: 0.8855 (p) cc_final: 0.8401 (p) REVERT: B 174 ILE cc_start: 0.8032 (tt) cc_final: 0.6526 (tt) REVERT: B 233 PHE cc_start: 0.8259 (m-80) cc_final: 0.7455 (m-80) REVERT: B 432 ILE cc_start: 0.8929 (mt) cc_final: 0.8689 (mp) REVERT: B 490 LEU cc_start: 0.8346 (mt) cc_final: 0.7288 (mm) REVERT: B 526 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7289 (mt-10) REVERT: B 535 ILE cc_start: 0.8540 (mt) cc_final: 0.8303 (mt) REVERT: B 634 LYS cc_start: 0.8422 (mttt) cc_final: 0.8001 (mttm) REVERT: B 657 MET cc_start: 0.7952 (mmp) cc_final: 0.7639 (mmp) REVERT: B 684 PHE cc_start: 0.6915 (m-10) cc_final: 0.6198 (m-80) REVERT: B 722 ARG cc_start: 0.8980 (ttm170) cc_final: 0.8213 (ttm170) REVERT: D 404 THR cc_start: 0.8701 (m) cc_final: 0.8061 (p) REVERT: D 426 ARG cc_start: 0.8804 (ttt180) cc_final: 0.8542 (tpm170) REVERT: E 57 MET cc_start: 0.6131 (ttm) cc_final: 0.5752 (ttp) REVERT: E 79 ASN cc_start: 0.7622 (m-40) cc_final: 0.7416 (m-40) REVERT: E 186 ILE cc_start: 0.8629 (mt) cc_final: 0.8335 (mt) REVERT: E 221 VAL cc_start: 0.8971 (t) cc_final: 0.8507 (p) REVERT: F 8 LEU cc_start: 0.7972 (mt) cc_final: 0.7691 (mt) REVERT: F 49 LEU cc_start: 0.9406 (mt) cc_final: 0.9154 (mt) REVERT: F 130 GLU cc_start: 0.5293 (pt0) cc_final: 0.4971 (pt0) REVERT: F 158 LYS cc_start: 0.9049 (tptt) cc_final: 0.8749 (tptt) REVERT: F 165 LYS cc_start: 0.8457 (tmtt) cc_final: 0.8147 (tmtt) REVERT: F 169 ASP cc_start: 0.5662 (t0) cc_final: 0.4906 (p0) REVERT: F 203 LEU cc_start: 0.9248 (mt) cc_final: 0.8945 (mt) REVERT: F 215 LEU cc_start: 0.8918 (tp) cc_final: 0.8615 (tp) REVERT: G 9 LEU cc_start: 0.8976 (tp) cc_final: 0.8307 (tp) REVERT: G 11 GLU cc_start: 0.7717 (mp0) cc_final: 0.7371 (mp0) REVERT: G 54 GLN cc_start: 0.8920 (mt0) cc_final: 0.8685 (mm110) outliers start: 3 outliers final: 0 residues processed: 460 average time/residue: 0.1288 time to fit residues: 86.7557 Evaluate side-chains 328 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 7 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN A 595 ASN A 598 HIS A 621 ASN ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 ASN B 555 GLN ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN ** F 185 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 = 0.3775 r_free = 0.3775 target = 0.090564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076764 restraints weight = 90726.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.078160 restraints weight = 66849.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079199 restraints weight = 52453.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.079952 restraints weight = 43206.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080553 restraints weight = 37047.927| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17421 Z= 0.256 Angle : 1.037 66.866 23704 Z= 0.437 Chirality : 0.046 0.241 2879 Planarity : 0.006 0.071 3082 Dihedral : 6.598 43.039 2571 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.14 % Allowed : 4.92 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.78 (0.19), residues: 1702 helix: -0.38 (0.18), residues: 779 sheet: -2.37 (0.31), residues: 246 loop : -3.43 (0.20), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 695 TYR 0.034 0.003 TYR E 183 PHE 0.028 0.003 PHE F 50 TRP 0.018 0.002 TRP D 394 HIS 0.017 0.002 HIS B 700 Details of bonding type rmsd covalent geometry : bond 0.00531 (17417) covalent geometry : angle 0.85736 (23692) hydrogen bonds : bond 0.04604 ( 973) hydrogen bonds : angle 5.68012 ( 2859) metal coordination : bond 0.00907 ( 4) metal coordination : angle 25.97881 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 375 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.8095 (tttt) cc_final: 0.7677 (mmtm) REVERT: A 373 GLN cc_start: 0.9032 (pt0) cc_final: 0.8740 (pt0) REVERT: A 495 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8689 (tp30) REVERT: A 501 TYR cc_start: 0.8532 (p90) cc_final: 0.8298 (p90) REVERT: A 536 MET cc_start: 0.8287 (mtp) cc_final: 0.7749 (mtp) REVERT: A 606 PHE cc_start: 0.7973 (m-80) cc_final: 0.7472 (m-10) REVERT: A 623 LEU cc_start: 0.9362 (tp) cc_final: 0.9158 (tt) REVERT: A 625 GLN cc_start: 0.8865 (tt0) cc_final: 0.8617 (tt0) REVERT: A 650 MET cc_start: 0.6690 (ttp) cc_final: 0.6451 (ttt) REVERT: B 160 GLU cc_start: 0.9251 (tp30) cc_final: 0.8806 (tp30) REVERT: B 316 GLN cc_start: 0.8210 (mp-120) cc_final: 0.7985 (mm-40) REVERT: B 332 PHE cc_start: 0.8499 (m-10) cc_final: 0.8073 (m-10) REVERT: B 377 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8002 (tm-30) REVERT: B 432 ILE cc_start: 0.8941 (mt) cc_final: 0.8730 (mp) REVERT: B 526 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7339 (mt-10) REVERT: B 597 LEU cc_start: 0.6300 (pp) cc_final: 0.5821 (mp) REVERT: B 634 LYS cc_start: 0.8327 (mttt) cc_final: 0.7887 (mttm) REVERT: B 674 TYR cc_start: 0.7068 (m-80) cc_final: 0.6830 (m-80) REVERT: B 722 ARG cc_start: 0.8736 (ttm170) cc_final: 0.8283 (ttm170) REVERT: D 404 THR cc_start: 0.8601 (m) cc_final: 0.8366 (p) REVERT: D 426 ARG cc_start: 0.8921 (ttt180) cc_final: 0.8504 (tpm170) REVERT: D 441 MET cc_start: 0.7509 (mtm) cc_final: 0.7128 (mtm) REVERT: E 79 ASN cc_start: 0.7615 (m-40) cc_final: 0.7336 (m-40) REVERT: E 93 GLU cc_start: 0.8237 (tt0) cc_final: 0.8016 (tt0) REVERT: F 11 LEU cc_start: 0.9294 (tp) cc_final: 0.9050 (tp) REVERT: F 49 LEU cc_start: 0.9426 (mt) cc_final: 0.9076 (mt) REVERT: F 130 GLU cc_start: 0.5277 (pt0) cc_final: 0.4923 (pt0) REVERT: F 157 MET cc_start: 0.8639 (tpt) cc_final: 0.8353 (tpt) REVERT: F 158 LYS cc_start: 0.8920 (tptt) cc_final: 0.8581 (tptt) REVERT: F 195 VAL cc_start: 0.8131 (t) cc_final: 0.7928 (p) REVERT: F 215 LEU cc_start: 0.8718 (tp) cc_final: 0.8514 (tp) REVERT: G 9 LEU cc_start: 0.9070 (tp) cc_final: 0.8617 (tp) REVERT: G 55 GLU cc_start: 0.8314 (mp0) cc_final: 0.8030 (mp0) outliers start: 2 outliers final: 1 residues processed: 376 average time/residue: 0.1175 time to fit residues: 66.5212 Evaluate side-chains 295 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 136 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 203 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN A 598 HIS A 629 HIS B 164 HIS B 203 ASN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 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 = 0.3834 r_free = 0.3834 target = 0.093515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.078825 restraints weight = 84516.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.080348 restraints weight = 61911.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.081497 restraints weight = 48388.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.082353 restraints weight = 39627.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083032 restraints weight = 33871.459| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17421 Z= 0.149 Angle : 0.873 58.729 23704 Z= 0.361 Chirality : 0.042 0.177 2879 Planarity : 0.005 0.070 3082 Dihedral : 5.892 34.201 2571 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.19), residues: 1702 helix: 0.14 (0.18), residues: 782 sheet: -2.08 (0.33), residues: 228 loop : -3.28 (0.20), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 335 TYR 0.023 0.002 TYR A 534 PHE 0.036 0.002 PHE B 539 TRP 0.013 0.001 TRP F 22 HIS 0.012 0.001 HIS B 700 Details of bonding type rmsd covalent geometry : bond 0.00316 (17417) covalent geometry : angle 0.70591 (23692) hydrogen bonds : bond 0.03826 ( 973) hydrogen bonds : angle 5.10360 ( 2859) metal coordination : bond 0.00764 ( 4) metal coordination : angle 22.85491 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 401 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.8334 (tttt) cc_final: 0.7703 (mmtm) REVERT: A 327 MET cc_start: 0.8783 (tpp) cc_final: 0.8105 (tpp) REVERT: A 412 MET cc_start: 0.8800 (pmm) cc_final: 0.7752 (pmm) REVERT: A 438 MET cc_start: 0.8268 (mtt) cc_final: 0.7925 (mtt) REVERT: A 450 MET cc_start: 0.8604 (mpp) cc_final: 0.8180 (tpt) REVERT: A 501 TYR cc_start: 0.8198 (p90) cc_final: 0.7721 (p90) REVERT: A 533 LEU cc_start: 0.8641 (mt) cc_final: 0.8364 (mt) REVERT: A 606 PHE cc_start: 0.7980 (m-80) cc_final: 0.7720 (m-10) REVERT: A 625 GLN cc_start: 0.8850 (tt0) cc_final: 0.8091 (tm-30) REVERT: A 650 MET cc_start: 0.6663 (ttp) cc_final: 0.6368 (ttt) REVERT: A 696 MET cc_start: 0.6284 (mtp) cc_final: 0.5854 (ttt) REVERT: B 94 TYR cc_start: 0.6995 (p90) cc_final: 0.6481 (p90) REVERT: B 105 LEU cc_start: 0.8188 (tp) cc_final: 0.7922 (tp) REVERT: B 160 GLU cc_start: 0.9255 (tp30) cc_final: 0.8479 (tp30) REVERT: B 233 PHE cc_start: 0.8146 (m-80) cc_final: 0.7942 (m-80) REVERT: B 377 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7870 (tm-30) REVERT: B 406 LEU cc_start: 0.9392 (mt) cc_final: 0.9171 (mt) REVERT: B 419 GLU cc_start: 0.7338 (tm-30) cc_final: 0.7013 (tm-30) REVERT: B 432 ILE cc_start: 0.9087 (mt) cc_final: 0.8794 (mp) REVERT: B 447 VAL cc_start: 0.9186 (t) cc_final: 0.8922 (t) REVERT: B 634 LYS cc_start: 0.8206 (mttt) cc_final: 0.7679 (mttm) REVERT: B 674 TYR cc_start: 0.7060 (m-80) cc_final: 0.6859 (m-80) REVERT: B 712 GLU cc_start: 0.9205 (tp30) cc_final: 0.8929 (tp30) REVERT: D 387 ILE cc_start: 0.9074 (mm) cc_final: 0.8777 (mm) REVERT: D 392 ARG cc_start: 0.9178 (ttm110) cc_final: 0.8663 (tpm170) REVERT: D 426 ARG cc_start: 0.8906 (ttt180) cc_final: 0.8480 (tpm170) REVERT: E 93 GLU cc_start: 0.8327 (tt0) cc_final: 0.8093 (tt0) REVERT: E 126 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8647 (ttpp) REVERT: E 137 MET cc_start: 0.6916 (tpp) cc_final: 0.6619 (tpp) REVERT: F 130 GLU cc_start: 0.5160 (pt0) cc_final: 0.4864 (pt0) REVERT: F 157 MET cc_start: 0.8686 (tpt) cc_final: 0.8434 (tpt) REVERT: F 158 LYS cc_start: 0.8972 (tptt) cc_final: 0.8358 (tptt) REVERT: G 9 LEU cc_start: 0.8799 (tp) cc_final: 0.8396 (tp) REVERT: G 55 GLU cc_start: 0.8316 (mp0) cc_final: 0.7837 (mp0) outliers start: 1 outliers final: 0 residues processed: 402 average time/residue: 0.1219 time to fit residues: 73.4452 Evaluate side-chains 306 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 54 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN A 598 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 210 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 227 HIS ** F 185 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 = 0.3743 r_free = 0.3743 target = 0.088471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.074710 restraints weight = 88395.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.076055 restraints weight = 65659.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.077049 restraints weight = 51931.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.077801 restraints weight = 43079.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.078378 restraints weight = 37149.898| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17421 Z= 0.290 Angle : 1.080 68.579 23704 Z= 0.451 Chirality : 0.046 0.232 2879 Planarity : 0.006 0.078 3082 Dihedral : 6.440 37.785 2571 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.07 % Allowed : 4.22 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (0.19), residues: 1702 helix: -0.25 (0.18), residues: 785 sheet: -2.17 (0.31), residues: 245 loop : -3.40 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 642 TYR 0.030 0.003 TYR B 639 PHE 0.027 0.003 PHE B 157 TRP 0.019 0.003 TRP A 435 HIS 0.011 0.002 HIS D 448 Details of bonding type rmsd covalent geometry : bond 0.00602 (17417) covalent geometry : angle 0.88091 (23692) hydrogen bonds : bond 0.04596 ( 973) hydrogen bonds : angle 5.72284 ( 2859) metal coordination : bond 0.01126 ( 4) metal coordination : angle 27.81696 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.8553 (tttt) cc_final: 0.8112 (mmtm) REVERT: A 327 MET cc_start: 0.9031 (tpp) cc_final: 0.8448 (tpp) REVERT: A 332 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7350 (mtp85) REVERT: A 412 MET cc_start: 0.8884 (pmm) cc_final: 0.7895 (pmm) REVERT: A 450 MET cc_start: 0.8768 (mpp) cc_final: 0.8434 (tpt) REVERT: A 495 GLU cc_start: 0.8635 (tp30) cc_final: 0.8221 (tp30) REVERT: A 533 LEU cc_start: 0.9055 (mt) cc_final: 0.8842 (mt) REVERT: A 536 MET cc_start: 0.7144 (ttm) cc_final: 0.6555 (ttm) REVERT: A 625 GLN cc_start: 0.8806 (tt0) cc_final: 0.8570 (tt0) REVERT: B 72 TYR cc_start: 0.8342 (t80) cc_final: 0.8009 (t80) REVERT: B 107 LEU cc_start: 0.8098 (mt) cc_final: 0.7858 (mt) REVERT: B 160 GLU cc_start: 0.9476 (tp30) cc_final: 0.8948 (tp30) REVERT: B 377 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7672 (tm-30) REVERT: B 447 VAL cc_start: 0.9286 (t) cc_final: 0.8964 (t) REVERT: B 546 GLU cc_start: 0.7536 (mp0) cc_final: 0.7287 (mp0) REVERT: B 634 LYS cc_start: 0.8254 (mttt) cc_final: 0.7833 (mttm) REVERT: D 426 ARG cc_start: 0.8986 (ttt180) cc_final: 0.8598 (tpm170) REVERT: D 450 ASP cc_start: 0.7322 (t0) cc_final: 0.6779 (p0) REVERT: E 93 GLU cc_start: 0.8183 (tt0) cc_final: 0.7981 (tt0) REVERT: E 137 MET cc_start: 0.7310 (tpp) cc_final: 0.6765 (tpp) REVERT: F 48 HIS cc_start: 0.9172 (t70) cc_final: 0.8970 (t70) REVERT: F 49 LEU cc_start: 0.9414 (mt) cc_final: 0.9026 (mt) REVERT: F 158 LYS cc_start: 0.8836 (tptt) cc_final: 0.8621 (tptt) REVERT: F 169 ASP cc_start: 0.5567 (t0) cc_final: 0.5101 (p0) REVERT: G 13 ASP cc_start: 0.8500 (p0) cc_final: 0.8288 (p0) REVERT: G 55 GLU cc_start: 0.8186 (mp0) cc_final: 0.7710 (mp0) outliers start: 1 outliers final: 0 residues processed: 350 average time/residue: 0.1168 time to fit residues: 62.1082 Evaluate side-chains 272 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 147 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 HIS ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN A 598 HIS ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS E 235 HIS ** F 185 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 = 0.3745 r_free = 0.3745 target = 0.088415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.074713 restraints weight = 90062.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.076105 restraints weight = 66006.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.077104 restraints weight = 51658.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.077881 restraints weight = 42704.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.078470 restraints weight = 36628.148| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17421 Z= 0.261 Angle : 1.112 66.428 23704 Z= 0.436 Chirality : 0.046 0.305 2879 Planarity : 0.006 0.074 3082 Dihedral : 6.329 38.942 2571 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (0.19), residues: 1702 helix: -0.31 (0.18), residues: 788 sheet: -2.21 (0.31), residues: 238 loop : -3.29 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 185 TYR 0.027 0.003 TYR B 639 PHE 0.023 0.003 PHE A 518 TRP 0.020 0.002 TRP A 493 HIS 0.014 0.002 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00543 (17417) covalent geometry : angle 0.85075 (23692) hydrogen bonds : bond 0.04516 ( 973) hydrogen bonds : angle 5.68511 ( 2859) metal coordination : bond 0.00864 ( 4) metal coordination : angle 31.85625 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.8438 (tttt) cc_final: 0.8131 (mmtm) REVERT: A 332 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7721 (mtp85) REVERT: A 359 LYS cc_start: 0.8188 (tttp) cc_final: 0.7906 (mmtt) REVERT: A 377 GLN cc_start: 0.8679 (mt0) cc_final: 0.8369 (mt0) REVERT: A 412 MET cc_start: 0.8937 (pmm) cc_final: 0.7954 (pmm) REVERT: A 450 MET cc_start: 0.8522 (mpp) cc_final: 0.8134 (tpt) REVERT: A 495 GLU cc_start: 0.8641 (tp30) cc_final: 0.8189 (tp30) REVERT: A 536 MET cc_start: 0.7707 (ttm) cc_final: 0.6820 (ttm) REVERT: A 606 PHE cc_start: 0.7774 (m-80) cc_final: 0.7570 (m-10) REVERT: A 625 GLN cc_start: 0.8825 (tt0) cc_final: 0.8592 (tt0) REVERT: A 655 TYR cc_start: 0.7503 (p90) cc_final: 0.7302 (p90) REVERT: B 72 TYR cc_start: 0.8461 (t80) cc_final: 0.7891 (t80) REVERT: B 105 LEU cc_start: 0.8270 (tp) cc_final: 0.8024 (tp) REVERT: B 160 GLU cc_start: 0.9612 (tp30) cc_final: 0.8906 (tp30) REVERT: B 233 PHE cc_start: 0.8286 (m-80) cc_final: 0.8038 (m-80) REVERT: B 377 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7566 (tm-30) REVERT: B 418 ILE cc_start: 0.8706 (mm) cc_final: 0.8087 (pt) REVERT: B 634 LYS cc_start: 0.8454 (mttt) cc_final: 0.8035 (mttm) REVERT: D 426 ARG cc_start: 0.8947 (ttt180) cc_final: 0.8576 (tpm170) REVERT: D 450 ASP cc_start: 0.7298 (t0) cc_final: 0.6740 (p0) REVERT: E 93 GLU cc_start: 0.8124 (tt0) cc_final: 0.7847 (tt0) REVERT: E 137 MET cc_start: 0.7183 (tpp) cc_final: 0.6767 (tpp) REVERT: F 42 MET cc_start: 0.8317 (ptp) cc_final: 0.7975 (ptt) REVERT: F 48 HIS cc_start: 0.9068 (t70) cc_final: 0.8816 (t70) REVERT: F 49 LEU cc_start: 0.9381 (mt) cc_final: 0.8955 (mt) REVERT: F 130 GLU cc_start: 0.5496 (pt0) cc_final: 0.5276 (pt0) REVERT: F 157 MET cc_start: 0.8642 (tpt) cc_final: 0.8371 (tpt) REVERT: F 169 ASP cc_start: 0.6137 (t0) cc_final: 0.5130 (p0) REVERT: G 55 GLU cc_start: 0.8305 (mp0) cc_final: 0.7805 (mp0) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1208 time to fit residues: 62.2867 Evaluate side-chains 265 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 165 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 621 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.092255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.078195 restraints weight = 87007.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.079677 restraints weight = 63958.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.080752 restraints weight = 50056.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.081514 restraints weight = 41182.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.082206 restraints weight = 35477.635| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17421 Z= 0.150 Angle : 0.941 64.878 23704 Z= 0.370 Chirality : 0.043 0.256 2879 Planarity : 0.005 0.055 3082 Dihedral : 5.683 35.235 2571 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.20), residues: 1702 helix: 0.28 (0.18), residues: 786 sheet: -1.95 (0.31), residues: 245 loop : -3.16 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 280 TYR 0.033 0.002 TYR B 639 PHE 0.024 0.002 PHE B 157 TRP 0.021 0.002 TRP F 22 HIS 0.007 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00314 (17417) covalent geometry : angle 0.72647 (23692) hydrogen bonds : bond 0.03826 ( 973) hydrogen bonds : angle 5.09406 ( 2859) metal coordination : bond 0.01381 ( 4) metal coordination : angle 26.61777 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.8345 (tttt) cc_final: 0.8093 (mmtm) REVERT: A 332 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7523 (mtp85) REVERT: A 407 ILE cc_start: 0.9650 (mm) cc_final: 0.9310 (pt) REVERT: A 412 MET cc_start: 0.8929 (pmm) cc_final: 0.7789 (pmm) REVERT: A 450 MET cc_start: 0.8435 (mpp) cc_final: 0.8019 (tpt) REVERT: A 495 GLU cc_start: 0.8510 (tp30) cc_final: 0.8215 (tp30) REVERT: A 533 LEU cc_start: 0.8821 (mt) cc_final: 0.8596 (mt) REVERT: A 536 MET cc_start: 0.7104 (ttm) cc_final: 0.6600 (ttm) REVERT: A 590 MET cc_start: 0.9201 (mpp) cc_final: 0.8999 (mpp) REVERT: A 606 PHE cc_start: 0.7705 (m-80) cc_final: 0.7429 (m-10) REVERT: A 625 GLN cc_start: 0.8801 (tt0) cc_final: 0.8081 (tm-30) REVERT: A 655 TYR cc_start: 0.7396 (p90) cc_final: 0.7194 (p90) REVERT: B 72 TYR cc_start: 0.8360 (t80) cc_final: 0.7968 (t80) REVERT: B 105 LEU cc_start: 0.7987 (tp) cc_final: 0.7704 (tp) REVERT: B 107 LEU cc_start: 0.7739 (mt) cc_final: 0.7395 (mt) REVERT: B 233 PHE cc_start: 0.8223 (m-80) cc_final: 0.7855 (m-80) REVERT: B 377 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7637 (tm-30) REVERT: B 418 ILE cc_start: 0.8625 (mm) cc_final: 0.8060 (pt) REVERT: B 419 GLU cc_start: 0.7405 (tm-30) cc_final: 0.6998 (tm-30) REVERT: B 546 GLU cc_start: 0.7372 (mp0) cc_final: 0.7130 (mp0) REVERT: B 634 LYS cc_start: 0.8213 (mttt) cc_final: 0.7810 (mttm) REVERT: B 657 MET cc_start: 0.8325 (mmp) cc_final: 0.7457 (mmm) REVERT: D 426 ARG cc_start: 0.8929 (ttt180) cc_final: 0.8554 (tpm170) REVERT: D 450 ASP cc_start: 0.7246 (t0) cc_final: 0.6671 (p0) REVERT: E 93 GLU cc_start: 0.8138 (tt0) cc_final: 0.7911 (tt0) REVERT: E 137 MET cc_start: 0.7033 (tpp) cc_final: 0.6671 (tpp) REVERT: F 130 GLU cc_start: 0.5163 (pt0) cc_final: 0.4911 (pt0) REVERT: F 158 LYS cc_start: 0.9011 (tptm) cc_final: 0.8664 (tptt) REVERT: F 169 ASP cc_start: 0.5382 (t0) cc_final: 0.4879 (p0) REVERT: F 181 ILE cc_start: 0.9188 (mt) cc_final: 0.8980 (mm) REVERT: F 215 LEU cc_start: 0.8725 (tp) cc_final: 0.8510 (tp) REVERT: G 10 ILE cc_start: 0.9342 (mm) cc_final: 0.8916 (mm) REVERT: G 13 ASP cc_start: 0.8300 (p0) cc_final: 0.7848 (p0) REVERT: G 55 GLU cc_start: 0.8406 (mp0) cc_final: 0.7922 (mp0) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.1220 time to fit residues: 66.6965 Evaluate side-chains 275 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 168 optimal weight: 0.9990 chunk 224 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 238 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.086047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.072693 restraints weight = 90534.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.074054 restraints weight = 66038.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.075042 restraints weight = 51589.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.075777 restraints weight = 42311.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.076326 restraints weight = 36226.772| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 17421 Z= 0.355 Angle : 1.258 67.666 23704 Z= 0.515 Chirality : 0.051 0.275 2879 Planarity : 0.006 0.065 3082 Dihedral : 6.759 38.330 2571 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 27.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.19), residues: 1702 helix: -0.65 (0.17), residues: 793 sheet: -2.13 (0.31), residues: 240 loop : -3.41 (0.21), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 298 TYR 0.036 0.004 TYR B 639 PHE 0.025 0.003 PHE B 161 TRP 0.035 0.004 TRP A 493 HIS 0.012 0.003 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00738 (17417) covalent geometry : angle 1.00468 (23692) hydrogen bonds : bond 0.05261 ( 973) hydrogen bonds : angle 6.23595 ( 2859) metal coordination : bond 0.01163 ( 4) metal coordination : angle 33.65136 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.9271 (mp0) cc_final: 0.8751 (mp0) REVERT: A 377 GLN cc_start: 0.8743 (mt0) cc_final: 0.8481 (mt0) REVERT: A 412 MET cc_start: 0.9167 (pmm) cc_final: 0.8578 (pmm) REVERT: A 495 GLU cc_start: 0.8488 (tp30) cc_final: 0.8087 (tp30) REVERT: A 511 TRP cc_start: 0.7568 (p-90) cc_final: 0.7346 (p-90) REVERT: A 533 LEU cc_start: 0.9176 (mt) cc_final: 0.8934 (mt) REVERT: A 536 MET cc_start: 0.7669 (ttm) cc_final: 0.7065 (ttm) REVERT: A 606 PHE cc_start: 0.7471 (m-80) cc_final: 0.7158 (m-80) REVERT: A 625 GLN cc_start: 0.8815 (tt0) cc_final: 0.8390 (tt0) REVERT: A 655 TYR cc_start: 0.7653 (p90) cc_final: 0.7081 (p90) REVERT: A 712 LEU cc_start: 0.8519 (tt) cc_final: 0.7993 (tt) REVERT: B 94 TYR cc_start: 0.7367 (p90) cc_final: 0.7105 (p90) REVERT: B 105 LEU cc_start: 0.8543 (tp) cc_final: 0.8265 (tp) REVERT: B 357 PHE cc_start: 0.8577 (t80) cc_final: 0.8124 (t80) REVERT: B 377 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7669 (tm-30) REVERT: B 418 ILE cc_start: 0.8891 (mm) cc_final: 0.8236 (pt) REVERT: B 546 GLU cc_start: 0.7563 (mp0) cc_final: 0.7328 (mp0) REVERT: B 634 LYS cc_start: 0.8508 (mttt) cc_final: 0.8078 (mttm) REVERT: B 674 TYR cc_start: 0.6865 (m-80) cc_final: 0.6567 (m-80) REVERT: D 426 ARG cc_start: 0.8961 (ttt180) cc_final: 0.8597 (tpm170) REVERT: E 99 ASN cc_start: 0.8164 (m110) cc_final: 0.7711 (m110) REVERT: E 137 MET cc_start: 0.7261 (tpp) cc_final: 0.6912 (tpp) REVERT: F 42 MET cc_start: 0.8851 (ptt) cc_final: 0.8570 (ptt) REVERT: F 48 HIS cc_start: 0.9023 (t70) cc_final: 0.8435 (t-90) REVERT: F 130 GLU cc_start: 0.5747 (pt0) cc_final: 0.5432 (pt0) REVERT: F 143 TYR cc_start: 0.8475 (t80) cc_final: 0.8216 (t80) REVERT: F 157 MET cc_start: 0.8719 (tpt) cc_final: 0.8455 (tpt) REVERT: F 169 ASP cc_start: 0.6526 (t0) cc_final: 0.5204 (p0) REVERT: G 55 GLU cc_start: 0.8398 (mp0) cc_final: 0.8041 (mp0) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1181 time to fit residues: 57.6764 Evaluate side-chains 245 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 153 optimal weight: 0.8980 chunk 178 optimal weight: 9.9990 chunk 198 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS B 474 HIS ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.089249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.075425 restraints weight = 87762.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.076851 restraints weight = 64270.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.077895 restraints weight = 50272.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.078678 restraints weight = 41409.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.079292 restraints weight = 35360.222| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17421 Z= 0.200 Angle : 1.061 69.045 23704 Z= 0.415 Chirality : 0.046 0.227 2879 Planarity : 0.005 0.071 3082 Dihedral : 6.078 37.144 2571 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.19), residues: 1702 helix: -0.23 (0.18), residues: 791 sheet: -2.16 (0.30), residues: 252 loop : -3.21 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 392 TYR 0.036 0.002 TYR B 639 PHE 0.027 0.002 PHE B 157 TRP 0.016 0.002 TRP D 394 HIS 0.008 0.002 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00431 (17417) covalent geometry : angle 0.81210 (23692) hydrogen bonds : bond 0.04323 ( 973) hydrogen bonds : angle 5.55145 ( 2859) metal coordination : bond 0.00355 ( 4) metal coordination : angle 30.33492 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7618 (mtp85) REVERT: A 372 GLU cc_start: 0.9168 (mp0) cc_final: 0.8579 (mp0) REVERT: A 412 MET cc_start: 0.9034 (pmm) cc_final: 0.8341 (pmm) REVERT: A 495 GLU cc_start: 0.8506 (tp30) cc_final: 0.8222 (tp30) REVERT: A 501 TYR cc_start: 0.8150 (p90) cc_final: 0.7866 (p90) REVERT: A 533 LEU cc_start: 0.9079 (mt) cc_final: 0.8831 (mt) REVERT: A 536 MET cc_start: 0.7368 (ttm) cc_final: 0.6818 (ttm) REVERT: A 606 PHE cc_start: 0.7518 (m-80) cc_final: 0.7199 (m-80) REVERT: A 625 GLN cc_start: 0.8954 (tt0) cc_final: 0.8515 (tt0) REVERT: A 655 TYR cc_start: 0.7561 (p90) cc_final: 0.7359 (p90) REVERT: A 660 TYR cc_start: 0.8648 (m-80) cc_final: 0.8369 (m-80) REVERT: A 712 LEU cc_start: 0.8458 (tt) cc_final: 0.7983 (tt) REVERT: B 72 TYR cc_start: 0.8272 (t80) cc_final: 0.7331 (t80) REVERT: B 94 TYR cc_start: 0.7724 (p90) cc_final: 0.7456 (p90) REVERT: B 105 LEU cc_start: 0.8152 (tp) cc_final: 0.7930 (tp) REVERT: B 280 ARG cc_start: 0.8109 (mpp-170) cc_final: 0.7753 (ptp-170) REVERT: B 377 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7554 (tm-30) REVERT: B 418 ILE cc_start: 0.8799 (mm) cc_final: 0.8152 (pt) REVERT: B 546 GLU cc_start: 0.7521 (mp0) cc_final: 0.7302 (mp0) REVERT: B 634 LYS cc_start: 0.8253 (mttt) cc_final: 0.7809 (mttm) REVERT: B 674 TYR cc_start: 0.6730 (m-80) cc_final: 0.6330 (m-80) REVERT: D 392 ARG cc_start: 0.9135 (ttm110) cc_final: 0.8669 (tpm170) REVERT: D 426 ARG cc_start: 0.8935 (ttt180) cc_final: 0.8562 (tpm170) REVERT: D 441 MET cc_start: 0.7485 (mtt) cc_final: 0.7121 (mtt) REVERT: E 95 TYR cc_start: 0.8544 (t80) cc_final: 0.8249 (t80) REVERT: F 42 MET cc_start: 0.8771 (ptt) cc_final: 0.8474 (ptt) REVERT: F 130 GLU cc_start: 0.5335 (pt0) cc_final: 0.5106 (pt0) REVERT: F 157 MET cc_start: 0.8774 (tpt) cc_final: 0.8456 (tpt) REVERT: F 158 LYS cc_start: 0.9064 (tptm) cc_final: 0.8642 (tptt) REVERT: G 9 LEU cc_start: 0.8746 (tp) cc_final: 0.8539 (tp) REVERT: G 55 GLU cc_start: 0.8409 (mp0) cc_final: 0.7980 (mp0) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.1178 time to fit residues: 59.4524 Evaluate side-chains 255 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS B 474 HIS B 723 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.090637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.077118 restraints weight = 89668.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.078493 restraints weight = 65992.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.079491 restraints weight = 51928.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.080256 restraints weight = 42908.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.080828 restraints weight = 36869.118| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17421 Z= 0.173 Angle : 1.003 67.662 23704 Z= 0.397 Chirality : 0.044 0.220 2879 Planarity : 0.005 0.060 3082 Dihedral : 5.801 36.618 2571 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.19), residues: 1702 helix: -0.06 (0.18), residues: 795 sheet: -2.06 (0.31), residues: 250 loop : -3.17 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 56 TYR 0.038 0.002 TYR F 174 PHE 0.030 0.002 PHE B 157 TRP 0.014 0.002 TRP D 394 HIS 0.007 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00376 (17417) covalent geometry : angle 0.77663 (23692) hydrogen bonds : bond 0.04072 ( 973) hydrogen bonds : angle 5.34967 ( 2859) metal coordination : bond 0.00557 ( 4) metal coordination : angle 28.18960 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.5326 (m-30) cc_final: 0.5098 (m-30) REVERT: A 332 ARG cc_start: 0.8118 (mtt180) cc_final: 0.7629 (mtp85) REVERT: A 372 GLU cc_start: 0.9167 (mp0) cc_final: 0.8575 (mp0) REVERT: A 407 ILE cc_start: 0.9684 (mm) cc_final: 0.9334 (pt) REVERT: A 412 MET cc_start: 0.8996 (pmm) cc_final: 0.8729 (pmm) REVERT: A 495 GLU cc_start: 0.8642 (tp30) cc_final: 0.8244 (tp30) REVERT: A 501 TYR cc_start: 0.7961 (p90) cc_final: 0.7742 (p90) REVERT: A 533 LEU cc_start: 0.8997 (mt) cc_final: 0.8783 (mt) REVERT: A 536 MET cc_start: 0.7448 (ttm) cc_final: 0.7212 (ttm) REVERT: A 606 PHE cc_start: 0.7565 (m-80) cc_final: 0.7234 (m-80) REVERT: A 625 GLN cc_start: 0.8971 (tt0) cc_final: 0.8533 (tt0) REVERT: A 655 TYR cc_start: 0.7437 (p90) cc_final: 0.7220 (p90) REVERT: A 660 TYR cc_start: 0.8606 (m-80) cc_final: 0.8357 (m-80) REVERT: A 712 LEU cc_start: 0.8488 (tt) cc_final: 0.8007 (tt) REVERT: B 72 TYR cc_start: 0.8203 (t80) cc_final: 0.7776 (t80) REVERT: B 94 TYR cc_start: 0.7957 (p90) cc_final: 0.7617 (p90) REVERT: B 105 LEU cc_start: 0.8203 (tp) cc_final: 0.7960 (tp) REVERT: B 233 PHE cc_start: 0.8380 (m-80) cc_final: 0.7908 (m-10) REVERT: B 280 ARG cc_start: 0.8165 (mpp-170) cc_final: 0.7864 (ptp-170) REVERT: B 357 PHE cc_start: 0.8444 (t80) cc_final: 0.7714 (t80) REVERT: B 377 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7494 (tm-30) REVERT: B 418 ILE cc_start: 0.8765 (mm) cc_final: 0.8109 (pt) REVERT: B 419 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7185 (tm-30) REVERT: B 447 VAL cc_start: 0.9222 (t) cc_final: 0.8943 (t) REVERT: B 493 MET cc_start: 0.7927 (tmm) cc_final: 0.7591 (tmm) REVERT: B 634 LYS cc_start: 0.8158 (mttt) cc_final: 0.7527 (mttm) REVERT: B 674 TYR cc_start: 0.6698 (m-80) cc_final: 0.6255 (m-80) REVERT: D 387 ILE cc_start: 0.8951 (mm) cc_final: 0.8639 (mm) REVERT: D 426 ARG cc_start: 0.8958 (ttt180) cc_final: 0.8557 (tpm170) REVERT: D 441 MET cc_start: 0.7461 (mtt) cc_final: 0.7202 (mtt) REVERT: E 95 TYR cc_start: 0.8330 (t80) cc_final: 0.8074 (t80) REVERT: E 137 MET cc_start: 0.6984 (tpp) cc_final: 0.6023 (tpp) REVERT: E 139 CYS cc_start: 0.8388 (m) cc_final: 0.8038 (m) REVERT: F 42 MET cc_start: 0.8759 (ptt) cc_final: 0.8452 (ptt) REVERT: G 9 LEU cc_start: 0.9014 (tp) cc_final: 0.8627 (tp) REVERT: G 55 GLU cc_start: 0.8339 (mp0) cc_final: 0.8010 (mp0) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1220 time to fit residues: 63.9327 Evaluate side-chains 265 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 201 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 184 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 240 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 ASN ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS B 474 HIS D 390 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.090393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.076647 restraints weight = 85815.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.078060 restraints weight = 63151.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.079110 restraints weight = 49501.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.079894 restraints weight = 40735.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.080314 restraints weight = 34876.270| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.6453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17421 Z= 0.172 Angle : 0.997 68.542 23704 Z= 0.394 Chirality : 0.044 0.282 2879 Planarity : 0.005 0.067 3082 Dihedral : 5.700 36.414 2571 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.20), residues: 1702 helix: 0.00 (0.18), residues: 800 sheet: -1.96 (0.31), residues: 255 loop : -3.21 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 56 TYR 0.038 0.002 TYR F 174 PHE 0.033 0.002 PHE B 157 TRP 0.015 0.002 TRP A 493 HIS 0.006 0.001 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00373 (17417) covalent geometry : angle 0.76843 (23692) hydrogen bonds : bond 0.04032 ( 973) hydrogen bonds : angle 5.28466 ( 2859) metal coordination : bond 0.01068 ( 4) metal coordination : angle 28.22462 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2751.77 seconds wall clock time: 48 minutes 17.86 seconds (2897.86 seconds total)