Starting phenix.real_space_refine on Fri Mar 6 12:16:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z6p_11102/03_2026/6z6p_11102.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z6p_11102/03_2026/6z6p_11102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6z6p_11102/03_2026/6z6p_11102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z6p_11102/03_2026/6z6p_11102.map" model { file = "/net/cci-nas-00/data/ceres_data/6z6p_11102/03_2026/6z6p_11102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z6p_11102/03_2026/6z6p_11102.cif" } resolution = 4.43 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= 0.008 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 288 5.49 5 S 100 5.16 5 C 18784 2.51 5 N 5486 2.21 5 O 6455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31115 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5178 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 615} Chain breaks: 2 Chain: "L" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5245 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4376 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Chain breaks: 3 Chain: "N" Number of atoms: 4416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4416 Classifications: {'peptide': 541} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 520} Chain breaks: 6 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.33, per 1000 atoms: 0.20 Number of scatterers: 31115 At special positions: 0 Unit cell: (127.68, 149.811, 264.723, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 100 16.00 P 288 15.00 O 6455 8.00 N 5486 7.00 C 18784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 359 " - pdb=" SG CYS N 366 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" NE2 HIS K 205 " pdb=" ZN L 801 " pdb="ZN ZN L 801 " - pdb=" ND1 HIS L 247 " 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5950 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 13 sheets defined 54.0% alpha, 5.7% beta 126 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'K' and resid 76 through 81 removed outlier: 3.797A pdb=" N ILE K 80 " --> pdb=" O TYR K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 99 removed outlier: 4.098A pdb=" N ARG K 92 " --> pdb=" O ARG K 88 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE K 93 " --> pdb=" O ARG K 89 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA K 98 " --> pdb=" O TYR K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 134 Processing helix chain 'K' and resid 136 through 146 removed outlier: 3.619A pdb=" N THR K 146 " --> pdb=" O PHE K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 161 removed outlier: 3.653A pdb=" N LEU K 154 " --> pdb=" O SER K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 190 removed outlier: 3.546A pdb=" N ARG K 175 " --> pdb=" O TYR K 171 " (cutoff:3.500A) Proline residue: K 177 - end of helix removed outlier: 3.787A pdb=" N ALA K 187 " --> pdb=" O GLU K 183 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU K 190 " --> pdb=" O LYS K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 232 removed outlier: 3.750A pdb=" N LEU K 229 " --> pdb=" O ALA K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 254 removed outlier: 4.214A pdb=" N LYS K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 257 No H-bonds generated for 'chain 'K' and resid 255 through 257' Processing helix chain 'K' and resid 289 through 293 removed outlier: 3.566A pdb=" N GLU K 293 " --> pdb=" O GLY K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 326 removed outlier: 3.903A pdb=" N TYR K 311 " --> pdb=" O GLY K 307 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET K 320 " --> pdb=" O GLU K 316 " (cutoff:3.500A) Proline residue: K 321 - end of helix Processing helix chain 'K' and resid 351 through 366 removed outlier: 3.692A pdb=" N TYR K 355 " --> pdb=" O THR K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 396 removed outlier: 4.238A pdb=" N ARG K 385 " --> pdb=" O ASP K 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER K 386 " --> pdb=" O ALA K 382 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS K 392 " --> pdb=" O LEU K 388 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL K 393 " --> pdb=" O SER K 389 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 415 removed outlier: 3.764A pdb=" N ILE K 414 " --> pdb=" O LYS K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 428 Processing helix chain 'K' and resid 429 through 432 Processing helix chain 'K' and resid 458 through 472 removed outlier: 3.686A pdb=" N ARG K 462 " --> pdb=" O GLN K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 534 through 544 removed outlier: 3.565A pdb=" N ILE K 538 " --> pdb=" O SER K 534 " (cutoff:3.500A) Processing helix chain 'K' and resid 562 through 578 Processing helix chain 'K' and resid 598 through 607 removed outlier: 4.270A pdb=" N ILE K 602 " --> pdb=" O SER K 598 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 645 Processing helix chain 'K' and resid 679 through 687 removed outlier: 3.591A pdb=" N ILE K 683 " --> pdb=" O GLY K 679 " (cutoff:3.500A) Processing helix chain 'K' and resid 687 through 699 removed outlier: 4.039A pdb=" N LEU K 696 " --> pdb=" O THR K 692 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 68 removed outlier: 3.506A pdb=" N MET L 66 " --> pdb=" O ASP L 63 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR L 68 " --> pdb=" O ARG L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 100 removed outlier: 3.645A pdb=" N ASN L 100 " --> pdb=" O ILE L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 136 through 147 removed outlier: 3.604A pdb=" N LEU L 140 " --> pdb=" O THR L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 161 Processing helix chain 'L' and resid 170 through 184 removed outlier: 3.972A pdb=" N ARG L 175 " --> pdb=" O TYR L 171 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU L 176 " --> pdb=" O ALA L 172 " (cutoff:3.500A) Proline residue: L 177 - end of helix Processing helix chain 'L' and resid 184 through 191 removed outlier: 3.686A pdb=" N VAL L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 226 Processing helix chain 'L' and resid 226 through 232 Processing helix chain 'L' and resid 249 through 254 removed outlier: 3.622A pdb=" N LYS L 254 " --> pdb=" O ASN L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 274 removed outlier: 3.687A pdb=" N LYS L 274 " --> pdb=" O GLU L 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 271 through 274' Processing helix chain 'L' and resid 307 through 318 removed outlier: 3.864A pdb=" N TYR L 311 " --> pdb=" O GLY L 307 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU L 316 " --> pdb=" O MET L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 318 through 327 removed outlier: 3.539A pdb=" N MET L 322 " --> pdb=" O VAL L 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 340 No H-bonds generated for 'chain 'L' and resid 338 through 340' Processing helix chain 'L' and resid 351 through 361 removed outlier: 3.534A pdb=" N TYR L 355 " --> pdb=" O THR L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 381 through 395 Processing helix chain 'L' and resid 410 through 421 removed outlier: 3.864A pdb=" N ILE L 414 " --> pdb=" O LYS L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 422 through 427 removed outlier: 3.741A pdb=" N SER L 425 " --> pdb=" O ARG L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 456 through 474 removed outlier: 3.575A pdb=" N ALA L 460 " --> pdb=" O PRO L 456 " (cutoff:3.500A) Processing helix chain 'L' and resid 532 through 543 removed outlier: 3.932A pdb=" N ASP L 536 " --> pdb=" O ASP L 532 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE L 537 " --> pdb=" O ASN L 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 580 Processing helix chain 'L' and resid 581 through 584 removed outlier: 3.768A pdb=" N PHE L 584 " --> pdb=" O ILE L 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 581 through 584' Processing helix chain 'L' and resid 599 through 609 Processing helix chain 'L' and resid 637 through 645 Processing helix chain 'L' and resid 681 through 699 removed outlier: 5.151A pdb=" N GLU L 689 " --> pdb=" O GLU L 685 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU L 690 " --> pdb=" O GLU L 686 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 43 Processing helix chain 'M' and resid 44 through 52 removed outlier: 3.762A pdb=" N HIS M 52 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 61 removed outlier: 4.172A pdb=" N ARG M 58 " --> pdb=" O SER M 54 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR M 59 " --> pdb=" O ASP M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 87 removed outlier: 3.950A pdb=" N SER M 82 " --> pdb=" O CYS M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 91 Processing helix chain 'M' and resid 104 through 113 Processing helix chain 'M' and resid 114 through 124 removed outlier: 3.647A pdb=" N ASP M 121 " --> pdb=" O SER M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 150 removed outlier: 3.737A pdb=" N LEU M 146 " --> pdb=" O THR M 142 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU M 150 " --> pdb=" O LEU M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 221 removed outlier: 3.946A pdb=" N GLN M 217 " --> pdb=" O GLN M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 255 removed outlier: 3.517A pdb=" N CYS M 247 " --> pdb=" O SER M 243 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS M 253 " --> pdb=" O LEU M 249 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS M 254 " --> pdb=" O PHE M 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 275 removed outlier: 4.012A pdb=" N VAL M 271 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE M 272 " --> pdb=" O ALA M 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 289 Processing helix chain 'M' and resid 295 through 300 Processing helix chain 'M' and resid 318 through 328 Processing helix chain 'M' and resid 405 through 441 removed outlier: 4.491A pdb=" N ASN M 409 " --> pdb=" O SER M 405 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS M 419 " --> pdb=" O GLY M 415 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS M 420 " --> pdb=" O ILE M 416 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU M 427 " --> pdb=" O GLN M 423 " (cutoff:3.500A) Processing helix chain 'M' and resid 449 through 465 removed outlier: 4.341A pdb=" N ASN M 458 " --> pdb=" O LYS M 454 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP M 460 " --> pdb=" O PHE M 456 " (cutoff:3.500A) Processing helix chain 'M' and resid 466 through 515 removed outlier: 3.877A pdb=" N ASN M 474 " --> pdb=" O VAL M 470 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN M 475 " --> pdb=" O LEU M 471 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS M 482 " --> pdb=" O LEU M 478 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN M 489 " --> pdb=" O GLU M 485 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE M 495 " --> pdb=" O LYS M 491 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY M 513 " --> pdb=" O LEU M 509 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU M 514 " --> pdb=" O MET M 510 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR M 515 " --> pdb=" O ALA M 511 " (cutoff:3.500A) Processing helix chain 'M' and resid 525 through 631 removed outlier: 4.181A pdb=" N THR M 545 " --> pdb=" O VAL M 541 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU M 546 " --> pdb=" O SER M 542 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU M 571 " --> pdb=" O GLU M 567 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU M 584 " --> pdb=" O SER M 580 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE M 591 " --> pdb=" O GLU M 587 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU M 596 " --> pdb=" O SER M 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 634 through 639 Processing helix chain 'N' and resid 20 through 34 removed outlier: 4.026A pdb=" N LEU N 25 " --> pdb=" O PHE N 21 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER N 26 " --> pdb=" O GLN N 22 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU N 27 " --> pdb=" O LYS N 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS N 33 " --> pdb=" O LEU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 42 Processing helix chain 'N' and resid 69 through 86 removed outlier: 3.966A pdb=" N ILE N 84 " --> pdb=" O ASN N 80 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN N 86 " --> pdb=" O ARG N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.685A pdb=" N LEU N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 103 removed outlier: 3.696A pdb=" N ARG N 102 " --> pdb=" O GLN N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 110 Processing helix chain 'N' and resid 113 through 128 removed outlier: 3.690A pdb=" N GLN N 117 " --> pdb=" O SER N 113 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU N 119 " --> pdb=" O LYS N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 154 removed outlier: 3.785A pdb=" N LEU N 151 " --> pdb=" O SER N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 159 removed outlier: 3.653A pdb=" N ILE N 158 " --> pdb=" O GLU N 155 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU N 159 " --> pdb=" O GLY N 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 155 through 159' Processing helix chain 'N' and resid 221 through 228 removed outlier: 3.719A pdb=" N LYS N 228 " --> pdb=" O LYS N 224 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 249 Processing helix chain 'N' and resid 272 through 280 removed outlier: 4.386A pdb=" N ASN N 280 " --> pdb=" O GLN N 276 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 307 Processing helix chain 'N' and resid 326 through 341 Processing helix chain 'N' and resid 354 through 362 Processing helix chain 'N' and resid 415 through 437 removed outlier: 4.269A pdb=" N HIS N 423 " --> pdb=" O THR N 419 " (cutoff:3.500A) Processing helix chain 'N' and resid 439 through 511 removed outlier: 4.302A pdb=" N LEU N 443 " --> pdb=" O GLY N 439 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER N 463 " --> pdb=" O GLU N 459 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY N 465 " --> pdb=" O LYS N 461 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS N 476 " --> pdb=" O GLN N 472 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER N 477 " --> pdb=" O GLU N 473 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE N 478 " --> pdb=" O VAL N 474 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS N 483 " --> pdb=" O ASN N 479 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU N 508 " --> pdb=" O LYS N 504 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU N 509 " --> pdb=" O ASN N 505 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN N 511 " --> pdb=" O GLN N 507 " (cutoff:3.500A) Processing helix chain 'N' and resid 517 through 523 Processing helix chain 'N' and resid 524 through 595 removed outlier: 4.047A pdb=" N ALA N 556 " --> pdb=" O GLU N 552 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER N 561 " --> pdb=" O ASN N 557 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS N 562 " --> pdb=" O ALA N 558 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU N 563 " --> pdb=" O GLU N 559 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU N 574 " --> pdb=" O LYS N 570 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER N 576 " --> pdb=" O GLN N 572 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS N 577 " --> pdb=" O ILE N 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.518A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.857A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.591A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.651A pdb=" N THR B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.973A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.038A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.939A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.701A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 119 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.849A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.820A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.001A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 77 Processing helix chain 'F' and resid 82 through 91 removed outlier: 3.516A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.587A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 removed outlier: 3.987A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 82 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.847A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 Processing sheet with id=AA1, first strand: chain 'K' and resid 118 through 120 removed outlier: 6.330A pdb=" N THR K 58 " --> pdb=" O LEU K 119 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER K 196 " --> pdb=" O VAL K 372 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU K 374 " --> pdb=" O SER K 196 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA K 198 " --> pdb=" O LEU K 374 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLY K 376 " --> pdb=" O ALA K 198 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS K 371 " --> pdb=" O VAL K 331 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE K 337 " --> pdb=" O GLU K 375 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY K 377 " --> pdb=" O PHE K 337 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET K 240 " --> pdb=" O ILE K 332 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER K 334 " --> pdb=" O MET K 240 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU K 242 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLY K 336 " --> pdb=" O LEU K 242 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE K 239 " --> pdb=" O LEU K 263 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL K 265 " --> pdb=" O ILE K 239 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE K 241 " --> pdb=" O VAL K 265 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU K 267 " --> pdb=" O ILE K 241 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP K 243 " --> pdb=" O LEU K 267 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N CYS K 297 " --> pdb=" O VAL K 262 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR K 264 " --> pdb=" O CYS K 297 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE K 299 " --> pdb=" O TYR K 264 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N SER K 266 " --> pdb=" O ILE K 299 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 476 through 477 removed outlier: 6.089A pdb=" N PHE K 592 " --> pdb=" O ILE K 619 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE K 621 " --> pdb=" O PHE K 592 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY K 594 " --> pdb=" O PHE K 621 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLY K 623 " --> pdb=" O GLY K 594 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU K 647 " --> pdb=" O ILE K 619 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE K 621 " --> pdb=" O LEU K 647 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE K 649 " --> pdb=" O PHE K 621 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU K 673 " --> pdb=" O SER K 646 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE K 648 " --> pdb=" O LEU K 673 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 511 through 516 removed outlier: 3.827A pdb=" N LYS K 515 " --> pdb=" O SER K 527 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER K 527 " --> pdb=" O LYS K 515 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 58 through 61 removed outlier: 5.976A pdb=" N THR L 58 " --> pdb=" O LEU L 119 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE L 121 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU L 60 " --> pdb=" O ILE L 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 296 through 301 removed outlier: 6.069A pdb=" N ILE L 239 " --> pdb=" O LEU L 263 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL L 265 " --> pdb=" O ILE L 239 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE L 241 " --> pdb=" O VAL L 265 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU L 267 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP L 243 " --> pdb=" O LEU L 267 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N ARG L 269 " --> pdb=" O ASP L 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 476 through 477 Processing sheet with id=AA7, first strand: chain 'L' and resid 547 through 548 Processing sheet with id=AA8, first strand: chain 'L' and resid 547 through 548 removed outlier: 4.303A pdb=" N ILE L 502 " --> pdb=" O LYS L 589 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP L 508 " --> pdb=" O ILE L 595 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE L 619 " --> pdb=" O ILE L 590 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE L 592 " --> pdb=" O ILE L 619 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE L 621 " --> pdb=" O PHE L 592 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLY L 594 " --> pdb=" O PHE L 621 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY L 623 " --> pdb=" O GLY L 594 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN L 620 " --> pdb=" O PHE L 649 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE L 648 " --> pdb=" O LEU L 673 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 31 through 35 removed outlier: 7.388A pdb=" N TYR M 31 " --> pdb=" O ARG M 237 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL M 239 " --> pdb=" O TYR M 31 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU M 33 " --> pdb=" O VAL M 239 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL M 136 " --> pdb=" O ILE M 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 13 removed outlier: 5.675A pdb=" N ALA N 142 " --> pdb=" O ILE N 262 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU N 238 " --> pdb=" O ARG N 164 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU N 240 " --> pdb=" O LYS N 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.347A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 83 through 84 removed outlier: 8.077A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 1162 hydrogen bonds defined for protein. 3435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 576 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 8.42 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5382 1.32 - 1.45: 9512 1.45 - 1.57: 16674 1.57 - 1.70: 576 1.70 - 1.82: 158 Bond restraints: 32302 Sorted by residual: bond pdb=" C MET L 320 " pdb=" N PRO L 321 " ideal model delta sigma weight residual 1.336 1.413 -0.077 1.20e-02 6.94e+03 4.11e+01 bond pdb=" CA CYS K 430 " pdb=" C CYS K 430 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.34e-02 5.57e+03 1.24e+01 bond pdb=" C GLU L 208 " pdb=" N PRO L 209 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" C3' DC I 66 " pdb=" O3' DC I 66 " ideal model delta sigma weight residual 1.422 1.518 -0.096 3.00e-02 1.11e+03 1.03e+01 bond pdb=" C3' DA J -55 " pdb=" O3' DA J -55 " ideal model delta sigma weight residual 1.422 1.327 0.095 3.00e-02 1.11e+03 9.96e+00 ... (remaining 32297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 42930 3.55 - 7.10: 1706 7.10 - 10.65: 212 10.65 - 14.20: 39 14.20 - 17.75: 13 Bond angle restraints: 44900 Sorted by residual: angle pdb=" C THR N 440 " pdb=" N VAL N 441 " pdb=" CA VAL N 441 " ideal model delta sigma weight residual 120.24 126.79 -6.55 6.30e-01 2.52e+00 1.08e+02 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" O5' DG J 21 " ideal model delta sigma weight residual 104.00 94.30 9.70 1.50e+00 4.44e-01 4.18e+01 angle pdb=" C3' DG I -53 " pdb=" O3' DG I -53 " pdb=" P DG I -52 " ideal model delta sigma weight residual 120.20 129.88 -9.68 1.50e+00 4.44e-01 4.17e+01 angle pdb=" C LEU L 555 " pdb=" N THR L 556 " pdb=" CA THR L 556 " ideal model delta sigma weight residual 121.54 133.48 -11.94 1.91e+00 2.74e-01 3.91e+01 angle pdb=" C THR B 30 " pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 120.58 128.76 -8.18 1.32e+00 5.74e-01 3.84e+01 ... (remaining 44895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.15: 16529 31.15 - 62.30: 2186 62.30 - 93.45: 122 93.45 - 124.60: 13 124.60 - 155.75: 4 Dihedral angle restraints: 18854 sinusoidal: 9662 harmonic: 9192 Sorted by residual: dihedral pdb=" CA SER K 54 " pdb=" C SER K 54 " pdb=" N PRO K 55 " pdb=" CA PRO K 55 " ideal model delta harmonic sigma weight residual 180.00 123.48 56.52 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA ILE N 306 " pdb=" C ILE N 306 " pdb=" N LYS N 307 " pdb=" CA LYS N 307 " ideal model delta harmonic sigma weight residual -180.00 -134.21 -45.79 0 5.00e+00 4.00e-02 8.39e+01 dihedral pdb=" CA PHE N 512 " pdb=" C PHE N 512 " pdb=" N ASN N 513 " pdb=" CA ASN N 513 " ideal model delta harmonic sigma weight residual -180.00 -136.05 -43.95 0 5.00e+00 4.00e-02 7.73e+01 ... (remaining 18851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4093 0.106 - 0.213: 825 0.213 - 0.319: 116 0.319 - 0.425: 19 0.425 - 0.531: 5 Chirality restraints: 5058 Sorted by residual: chirality pdb=" CB ILE L 530 " pdb=" CA ILE L 530 " pdb=" CG1 ILE L 530 " pdb=" CG2 ILE L 530 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CB VAL K 481 " pdb=" CA VAL K 481 " pdb=" CG1 VAL K 481 " pdb=" CG2 VAL K 481 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CB VAL L 518 " pdb=" CA VAL L 518 " pdb=" CG1 VAL L 518 " pdb=" CG2 VAL L 518 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 5055 not shown) Planarity restraints: 4730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 42 " 0.039 2.00e-02 2.50e+03 3.47e-02 2.71e+01 pdb=" N1 DC I 42 " -0.080 2.00e-02 2.50e+03 pdb=" C2 DC I 42 " 0.050 2.00e-02 2.50e+03 pdb=" O2 DC I 42 " -0.016 2.00e-02 2.50e+03 pdb=" N3 DC I 42 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DC I 42 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 42 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC I 42 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 42 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.010 2.00e-02 2.50e+03 3.10e-02 2.64e+01 pdb=" N9 DA I -35 " -0.062 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.075 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.017 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -23 " -0.037 2.00e-02 2.50e+03 3.27e-02 2.41e+01 pdb=" N1 DC I -23 " 0.081 2.00e-02 2.50e+03 pdb=" C2 DC I -23 " -0.039 2.00e-02 2.50e+03 pdb=" O2 DC I -23 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I -23 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DC I -23 " -0.000 2.00e-02 2.50e+03 pdb=" N4 DC I -23 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DC I -23 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DC I -23 " -0.006 2.00e-02 2.50e+03 ... (remaining 4727 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3041 2.74 - 3.28: 28291 3.28 - 3.82: 60627 3.82 - 4.36: 70846 4.36 - 4.90: 105744 Nonbonded interactions: 268549 Sorted by model distance: nonbonded pdb=" OD1 ASP L 245 " pdb="ZN ZN L 801 " model vdw 2.197 2.230 nonbonded pdb=" OD2 ASP K 245 " pdb="ZN ZN K 801 " model vdw 2.216 2.230 nonbonded pdb=" OD2 ASP L 338 " pdb="ZN ZN L 801 " model vdw 2.227 2.230 nonbonded pdb=" O4 DT I 3 " pdb=" O6 DG J -4 " model vdw 2.268 2.432 nonbonded pdb=" O GLN N 121 " pdb=" OG SER N 125 " model vdw 2.278 3.040 ... (remaining 268544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } ncs_group { reference = (chain 'K' and (resid 40 through 515 or (resid 516 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ )) or resid \ 517 through 656 or resid 667 through 678 or resid 680 through 801)) selection = (chain 'L' and (resid 40 through 439 or resid 445 through 801)) } 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=0.94 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: 14.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 36.230 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 0.010 0.098 32305 Z= 0.445 Angle : 1.617 17.750 44902 Z= 0.870 Chirality : 0.087 0.531 5058 Planarity : 0.011 0.090 4730 Dihedral : 23.433 155.755 12901 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.49 % Rotamer: Outliers : 1.29 % Allowed : 8.30 % Favored : 90.41 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 3.25 % Twisted General : 0.64 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.87 (0.11), residues: 3088 helix: -3.37 (0.08), residues: 1567 sheet: -2.23 (0.32), residues: 222 loop : -3.06 (0.14), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG G 88 TYR 0.051 0.005 TYR D 80 PHE 0.035 0.005 PHE L 592 TRP 0.039 0.005 TRP K 513 HIS 0.027 0.005 HIS K 507 Details of bonding type rmsd covalent geometry : bond 0.00964 (32302) covalent geometry : angle 1.61666 (44900) SS BOND : bond 0.00399 ( 1) SS BOND : angle 0.31140 ( 2) hydrogen bonds : bond 0.17336 ( 1470) hydrogen bonds : angle 7.92677 ( 4011) metal coordination : bond 0.06946 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 1.052 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: K 193 VAL cc_start: 0.6366 (m) cc_final: 0.6138 (m) REVERT: K 312 MET cc_start: 0.9455 (mmm) cc_final: 0.9029 (mmm) REVERT: L 60 LEU cc_start: 0.9715 (tt) cc_final: 0.9511 (pt) REVERT: L 149 MET cc_start: 0.5226 (mtt) cc_final: 0.5004 (mtp) REVERT: L 264 TYR cc_start: 0.9334 (t80) cc_final: 0.8628 (t80) REVERT: L 289 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8228 (tp30) REVERT: L 296 ASN cc_start: 0.9229 (t0) cc_final: 0.8711 (t0) REVERT: L 371 CYS cc_start: 0.9314 (p) cc_final: 0.8795 (t) REVERT: M 37 MET cc_start: 0.3530 (mtp) cc_final: 0.3039 (mtt) REVERT: N 251 TYR cc_start: 0.9125 (t80) cc_final: 0.8820 (p90) REVERT: N 260 MET cc_start: 0.9501 (ptm) cc_final: 0.9186 (ttp) REVERT: N 394 GLN cc_start: 0.9364 (mm110) cc_final: 0.9107 (pp30) REVERT: A 46 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.6990 (m) REVERT: B 84 MET cc_start: 0.9418 (mmm) cc_final: 0.9029 (tpp) REVERT: C 51 LEU cc_start: 0.8978 (tp) cc_final: 0.8666 (tp) REVERT: D 84 SER cc_start: 0.9379 (OUTLIER) cc_final: 0.8981 (p) REVERT: E 73 GLU cc_start: 0.8922 (tt0) cc_final: 0.8717 (tt0) REVERT: E 93 GLN cc_start: 0.9466 (tt0) cc_final: 0.9115 (tm-30) REVERT: E 94 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8701 (tp30) REVERT: E 100 LEU cc_start: 0.9519 (mt) cc_final: 0.9041 (pp) REVERT: F 84 MET cc_start: 0.9292 (mmm) cc_final: 0.8706 (tpp) REVERT: G 30 VAL cc_start: 0.9086 (t) cc_final: 0.8713 (p) outliers start: 36 outliers final: 4 residues processed: 263 average time/residue: 0.1970 time to fit residues: 82.4729 Evaluate side-chains 156 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN K 52 HIS K 247 HIS ** K 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 464 GLN ** K 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 500 ASN ** K 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS L 135 HIS ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 GLN L 286 GLN L 379 ASN ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 620 ASN ** L 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 682 ASN M 47 GLN M 124 ASN M 258 ASN M 316 GLN M 409 ASN M 477 ASN M 572 ASN N 72 GLN N 347 ASN ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 GLN N 500 ASN N 505 ASN N 554 GLN ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 620 ASN N 634 ASN A 39 HIS A 93 GLN C 31 HIS D 79 HIS D 92 GLN E 68 GLN E 93 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 64 ASN H 92 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.066293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.040400 restraints weight = 289575.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.041023 restraints weight = 242945.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.041549 restraints weight = 212499.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.041925 restraints weight = 194703.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.042139 restraints weight = 184280.814| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 32305 Z= 0.223 Angle : 0.794 10.106 44902 Z= 0.438 Chirality : 0.046 0.265 5058 Planarity : 0.006 0.091 4730 Dihedral : 26.781 162.436 6580 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.21 % Allowed : 4.08 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 1.63 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.13), residues: 3088 helix: -1.64 (0.11), residues: 1600 sheet: -2.33 (0.32), residues: 215 loop : -2.66 (0.15), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 201 TYR 0.032 0.002 TYR H 39 PHE 0.027 0.002 PHE E 67 TRP 0.013 0.002 TRP L 428 HIS 0.009 0.001 HIS L 52 Details of bonding type rmsd covalent geometry : bond 0.00468 (32302) covalent geometry : angle 0.79365 (44900) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.47760 ( 2) hydrogen bonds : bond 0.07868 ( 1470) hydrogen bonds : angle 5.62407 ( 4011) metal coordination : bond 0.00484 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 1.148 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: L 66 MET cc_start: 0.7014 (mtm) cc_final: 0.6812 (mtm) REVERT: L 107 THR cc_start: 0.7181 (p) cc_final: 0.6937 (t) REVERT: N 92 VAL cc_start: 0.7104 (OUTLIER) cc_final: 0.6835 (p) REVERT: N 260 MET cc_start: 0.8889 (ptm) cc_final: 0.8433 (ttp) REVERT: N 394 GLN cc_start: 0.9072 (mm110) cc_final: 0.8862 (pt0) REVERT: N 592 MET cc_start: 0.2993 (tpt) cc_final: 0.2734 (tpt) REVERT: D 59 MET cc_start: 0.9915 (mmm) cc_final: 0.9627 (tpp) REVERT: E 119 ILE cc_start: 0.7947 (pt) cc_final: 0.7245 (mm) REVERT: G 72 ASP cc_start: 0.9041 (p0) cc_final: 0.8799 (p0) outliers start: 6 outliers final: 1 residues processed: 181 average time/residue: 0.1897 time to fit residues: 56.0206 Evaluate side-chains 127 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 244 optimal weight: 10.0000 chunk 281 optimal weight: 0.0040 chunk 234 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 301 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 134 optimal weight: 30.0000 chunk 108 optimal weight: 1.9990 chunk 277 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN K 100 ASN ** K 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 645 ASN ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 293 HIS ** M 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 ASN N 449 ASN N 505 ASN ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 634 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.078013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.057575 restraints weight = 381224.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.058046 restraints weight = 309659.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.058360 restraints weight = 259361.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.058765 restraints weight = 234104.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.058935 restraints weight = 217247.113| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32305 Z= 0.185 Angle : 0.718 8.540 44902 Z= 0.395 Chirality : 0.044 0.237 5058 Planarity : 0.005 0.091 4730 Dihedral : 26.468 161.402 6580 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.11 % Allowed : 4.15 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.14), residues: 3088 helix: -0.78 (0.12), residues: 1604 sheet: -2.17 (0.33), residues: 207 loop : -2.41 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 237 TYR 0.034 0.002 TYR L 583 PHE 0.042 0.002 PHE K 315 TRP 0.017 0.002 TRP M 306 HIS 0.006 0.001 HIS K 247 Details of bonding type rmsd covalent geometry : bond 0.00395 (32302) covalent geometry : angle 0.71807 (44900) SS BOND : bond 0.00212 ( 1) SS BOND : angle 0.33780 ( 2) hydrogen bonds : bond 0.07012 ( 1470) hydrogen bonds : angle 5.09842 ( 4011) metal coordination : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 1.056 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: L 66 MET cc_start: 0.6958 (mtm) cc_final: 0.6657 (ttm) REVERT: L 107 THR cc_start: 0.7644 (p) cc_final: 0.7364 (t) REVERT: L 149 MET cc_start: 0.5300 (mtp) cc_final: 0.4960 (ptm) REVERT: N 260 MET cc_start: 0.8871 (ptm) cc_final: 0.8342 (ttp) REVERT: N 592 MET cc_start: 0.2971 (tpt) cc_final: 0.2741 (tpt) REVERT: D 59 MET cc_start: 0.9873 (mmm) cc_final: 0.9559 (tpp) REVERT: D 97 LEU cc_start: 0.9024 (mt) cc_final: 0.8727 (mt) REVERT: F 84 MET cc_start: 0.9299 (mmp) cc_final: 0.9081 (mmm) outliers start: 3 outliers final: 1 residues processed: 170 average time/residue: 0.1850 time to fit residues: 51.5015 Evaluate side-chains 124 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 193 optimal weight: 5.9990 chunk 326 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 290 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN K 83 HIS ** K 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 435 HIS ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 HIS ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 GLN L 369 ASN ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 ASN ** L 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 293 HIS ** M 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 20 GLN N 394 GLN N 505 ASN ** N 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN N 634 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.076928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.056395 restraints weight = 382042.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 84)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.056513 restraints weight = 316400.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.056836 restraints weight = 266055.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.057334 restraints weight = 240978.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.057526 restraints weight = 223611.306| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 32305 Z= 0.199 Angle : 0.696 8.672 44902 Z= 0.385 Chirality : 0.044 0.210 5058 Planarity : 0.005 0.075 4730 Dihedral : 26.224 159.011 6580 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.11 % Allowed : 3.94 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.14), residues: 3088 helix: -0.43 (0.12), residues: 1619 sheet: -2.32 (0.33), residues: 219 loop : -2.27 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 77 TYR 0.025 0.002 TYR K 276 PHE 0.021 0.002 PHE K 431 TRP 0.032 0.002 TRP M 32 HIS 0.011 0.001 HIS L 52 Details of bonding type rmsd covalent geometry : bond 0.00429 (32302) covalent geometry : angle 0.69626 (44900) SS BOND : bond 0.00240 ( 1) SS BOND : angle 0.24447 ( 2) hydrogen bonds : bond 0.07366 ( 1470) hydrogen bonds : angle 4.87692 ( 4011) metal coordination : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 1.056 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: K 312 MET cc_start: 0.9448 (mmp) cc_final: 0.9121 (mmm) REVERT: K 358 MET cc_start: 0.9047 (mtt) cc_final: 0.8775 (mtt) REVERT: L 66 MET cc_start: 0.6868 (mtm) cc_final: 0.6563 (ttm) REVERT: L 107 THR cc_start: 0.8192 (p) cc_final: 0.7862 (t) REVERT: L 149 MET cc_start: 0.5163 (mtp) cc_final: 0.4810 (ptp) REVERT: L 322 MET cc_start: 0.7991 (tpp) cc_final: 0.7733 (mmm) REVERT: N 103 MET cc_start: 0.6083 (mmp) cc_final: 0.5656 (mtm) REVERT: N 260 MET cc_start: 0.9018 (ptm) cc_final: 0.8537 (ttp) REVERT: D 56 MET cc_start: 0.8740 (ptp) cc_final: 0.8484 (ptp) outliers start: 3 outliers final: 0 residues processed: 151 average time/residue: 0.1775 time to fit residues: 44.5357 Evaluate side-chains 116 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 27 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 295 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 chunk 315 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN ** K 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 579 ASN ** K 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 GLN ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 394 GLN N 505 ASN N 524 ASN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN N 634 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.074491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.054053 restraints weight = 395048.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.054432 restraints weight = 328941.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.054706 restraints weight = 284694.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.054850 restraints weight = 255542.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.055195 restraints weight = 242142.241| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 32305 Z= 0.272 Angle : 0.759 11.412 44902 Z= 0.420 Chirality : 0.045 0.214 5058 Planarity : 0.005 0.081 4730 Dihedral : 26.313 164.016 6580 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 27.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.07 % Allowed : 3.61 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.14), residues: 3088 helix: -0.44 (0.12), residues: 1602 sheet: -2.36 (0.31), residues: 229 loop : -2.20 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 77 TYR 0.060 0.002 TYR N 571 PHE 0.027 0.002 PHE K 431 TRP 0.015 0.002 TRP L 513 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00581 (32302) covalent geometry : angle 0.75915 (44900) SS BOND : bond 0.00231 ( 1) SS BOND : angle 0.17412 ( 2) hydrogen bonds : bond 0.09136 ( 1470) hydrogen bonds : angle 5.02455 ( 4011) metal coordination : bond 0.00074 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.865 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: K 149 MET cc_start: -0.1259 (mtp) cc_final: -0.1599 (mtp) REVERT: K 312 MET cc_start: 0.9469 (mmp) cc_final: 0.9219 (mmm) REVERT: K 416 MET cc_start: 0.7822 (ttt) cc_final: 0.7505 (ttt) REVERT: L 107 THR cc_start: 0.7994 (p) cc_final: 0.7702 (t) REVERT: L 149 MET cc_start: 0.5189 (mtp) cc_final: 0.4865 (ptm) REVERT: L 358 MET cc_start: 0.8925 (mmt) cc_final: 0.8667 (mmt) outliers start: 2 outliers final: 0 residues processed: 145 average time/residue: 0.1698 time to fit residues: 41.7080 Evaluate side-chains 112 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 110 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 298 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 GLN ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN ** M 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 394 GLN N 497 ASN N 505 ASN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** 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 = 0.4040 r_free = 0.4040 target = 0.076168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.055988 restraints weight = 385009.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.056332 restraints weight = 324681.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.056523 restraints weight = 285057.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.056539 restraints weight = 278015.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.056644 restraints weight = 261613.212| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32305 Z= 0.183 Angle : 0.689 9.468 44902 Z= 0.380 Chirality : 0.044 0.229 5058 Planarity : 0.005 0.074 4730 Dihedral : 26.327 161.620 6580 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.04 % Allowed : 2.15 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.15), residues: 3088 helix: -0.12 (0.13), residues: 1602 sheet: -2.42 (0.31), residues: 232 loop : -2.06 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 39 TYR 0.044 0.002 TYR C 50 PHE 0.027 0.002 PHE N 37 TRP 0.016 0.002 TRP L 428 HIS 0.006 0.001 HIS K 247 Details of bonding type rmsd covalent geometry : bond 0.00396 (32302) covalent geometry : angle 0.68948 (44900) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.33709 ( 2) hydrogen bonds : bond 0.06823 ( 1470) hydrogen bonds : angle 4.82070 ( 4011) metal coordination : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.992 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: K 358 MET cc_start: 0.9054 (mtt) cc_final: 0.8714 (mtt) REVERT: K 416 MET cc_start: 0.7836 (ttt) cc_final: 0.7605 (ttt) REVERT: L 149 MET cc_start: 0.5047 (mtp) cc_final: 0.4715 (ptm) REVERT: L 358 MET cc_start: 0.8911 (mmt) cc_final: 0.8646 (mmt) REVERT: L 473 PHE cc_start: 0.9388 (m-80) cc_final: 0.9155 (p90) REVERT: N 260 MET cc_start: 0.9123 (ptm) cc_final: 0.8583 (ttm) REVERT: F 84 MET cc_start: 0.8991 (mmp) cc_final: 0.8768 (mmm) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.1759 time to fit residues: 43.6043 Evaluate side-chains 118 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 199 optimal weight: 0.1980 chunk 125 optimal weight: 0.0970 chunk 221 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 237 optimal weight: 0.0970 chunk 83 optimal weight: 20.0000 overall best weight: 1.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 GLN L 443 ASN L 464 GLN ** M 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 ASN N 394 GLN N 505 ASN N 583 GLN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.065320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.040017 restraints weight = 284952.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.040571 restraints weight = 250258.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.040801 restraints weight = 226392.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.041096 restraints weight = 213158.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.041234 restraints weight = 205241.182| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32305 Z= 0.151 Angle : 0.654 9.529 44902 Z= 0.359 Chirality : 0.042 0.226 5058 Planarity : 0.004 0.075 4730 Dihedral : 26.009 156.354 6580 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.04 % Allowed : 1.83 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 3088 helix: 0.20 (0.13), residues: 1607 sheet: -2.22 (0.32), residues: 234 loop : -1.95 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 76 TYR 0.028 0.002 TYR N 571 PHE 0.040 0.002 PHE L 475 TRP 0.032 0.002 TRP L 301 HIS 0.008 0.001 HIS L 69 Details of bonding type rmsd covalent geometry : bond 0.00324 (32302) covalent geometry : angle 0.65446 (44900) SS BOND : bond 0.00199 ( 1) SS BOND : angle 0.35091 ( 2) hydrogen bonds : bond 0.05984 ( 1470) hydrogen bonds : angle 4.55466 ( 4011) metal coordination : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.034 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: K 312 MET cc_start: 0.9507 (mmp) cc_final: 0.9306 (mmm) REVERT: L 149 MET cc_start: 0.4897 (mtp) cc_final: 0.4568 (ptp) REVERT: L 253 GLN cc_start: 0.3976 (OUTLIER) cc_final: 0.3744 (pt0) REVERT: L 542 LEU cc_start: 0.8898 (mt) cc_final: 0.8622 (mt) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.1757 time to fit residues: 47.2073 Evaluate side-chains 125 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 173 optimal weight: 7.9990 chunk 323 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 320 optimal weight: 6.9990 chunk 329 optimal weight: 8.9990 chunk 78 optimal weight: 0.0980 chunk 32 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 309 optimal weight: 10.0000 chunk 275 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 HIS ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS L 253 GLN L 268 HIS ** L 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 394 GLN N 505 ASN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN N 634 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.063688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.038341 restraints weight = 305246.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.038952 restraints weight = 254808.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.039357 restraints weight = 224916.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.039594 restraints weight = 206921.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.039933 restraints weight = 193946.324| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32305 Z= 0.206 Angle : 0.679 8.379 44902 Z= 0.374 Chirality : 0.043 0.247 5058 Planarity : 0.005 0.072 4730 Dihedral : 25.895 161.313 6580 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 3088 helix: 0.17 (0.13), residues: 1615 sheet: -2.24 (0.32), residues: 243 loop : -1.92 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 39 TYR 0.027 0.002 TYR K 276 PHE 0.017 0.002 PHE F 61 TRP 0.014 0.002 TRP M 298 HIS 0.006 0.001 HIS K 247 Details of bonding type rmsd covalent geometry : bond 0.00444 (32302) covalent geometry : angle 0.67880 (44900) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.26683 ( 2) hydrogen bonds : bond 0.07363 ( 1470) hydrogen bonds : angle 4.62410 ( 4011) metal coordination : bond 0.00051 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.006 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: K 312 MET cc_start: 0.9504 (mmp) cc_final: 0.9256 (mmm) REVERT: L 149 MET cc_start: 0.4837 (mtp) cc_final: 0.4545 (ptp) REVERT: L 358 MET cc_start: 0.8854 (mmt) cc_final: 0.8647 (mmt) REVERT: N 260 MET cc_start: 0.8804 (ptm) cc_final: 0.8249 (ttm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1752 time to fit residues: 43.5818 Evaluate side-chains 118 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 184 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 225 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 HIS L 369 ASN ** L 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS N 394 GLN N 449 ASN N 505 ASN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN ** N 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.061747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.037112 restraints weight = 305268.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.037676 restraints weight = 257476.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.038067 restraints weight = 228254.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.038253 restraints weight = 210085.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.038506 restraints weight = 200071.329| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 32305 Z= 0.239 Angle : 0.727 10.055 44902 Z= 0.400 Chirality : 0.044 0.258 5058 Planarity : 0.005 0.072 4730 Dihedral : 26.121 170.776 6580 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 26.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.15), residues: 3088 helix: -0.07 (0.12), residues: 1612 sheet: -2.29 (0.32), residues: 239 loop : -2.00 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 39 TYR 0.034 0.002 TYR C 50 PHE 0.018 0.002 PHE L 475 TRP 0.018 0.002 TRP M 298 HIS 0.007 0.002 HIS L 357 Details of bonding type rmsd covalent geometry : bond 0.00516 (32302) covalent geometry : angle 0.72656 (44900) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.30031 ( 2) hydrogen bonds : bond 0.08248 ( 1470) hydrogen bonds : angle 4.84587 ( 4011) metal coordination : bond 0.00147 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.132 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: K 312 MET cc_start: 0.9507 (mmp) cc_final: 0.9241 (mmm) REVERT: K 416 MET cc_start: 0.8411 (ttp) cc_final: 0.7320 (tmm) REVERT: L 66 MET cc_start: 0.6904 (ttt) cc_final: 0.6408 (tmm) REVERT: L 149 MET cc_start: 0.4778 (mtp) cc_final: 0.4440 (ptm) REVERT: N 260 MET cc_start: 0.8811 (ptm) cc_final: 0.8231 (ttm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1860 time to fit residues: 45.1365 Evaluate side-chains 116 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 242 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 119 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 301 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN ** K 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 620 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 GLN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 576 ASN N 394 GLN N 505 ASN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN N 634 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.061874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.037293 restraints weight = 306625.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.037809 restraints weight = 258784.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.038031 restraints weight = 231860.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.038385 restraints weight = 217514.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.038638 restraints weight = 206316.309| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32305 Z= 0.220 Angle : 0.717 14.728 44902 Z= 0.393 Chirality : 0.044 0.235 5058 Planarity : 0.005 0.073 4730 Dihedral : 26.220 179.931 6580 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 24.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.04 % Allowed : 0.50 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.15), residues: 3088 helix: -0.01 (0.13), residues: 1614 sheet: -2.35 (0.32), residues: 239 loop : -1.96 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 39 TYR 0.031 0.002 TYR K 276 PHE 0.017 0.002 PHE F 61 TRP 0.032 0.002 TRP N 391 HIS 0.009 0.001 HIS K 608 Details of bonding type rmsd covalent geometry : bond 0.00473 (32302) covalent geometry : angle 0.71720 (44900) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.32558 ( 2) hydrogen bonds : bond 0.07628 ( 1470) hydrogen bonds : angle 4.80927 ( 4011) metal coordination : bond 0.00130 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.053 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: K 312 MET cc_start: 0.9476 (mmp) cc_final: 0.9172 (mmm) REVERT: K 358 MET cc_start: 0.9337 (mtm) cc_final: 0.9083 (mtt) REVERT: K 416 MET cc_start: 0.8501 (ttp) cc_final: 0.8031 (ptm) REVERT: L 66 MET cc_start: 0.6413 (ttt) cc_final: 0.5766 (tmm) REVERT: L 149 MET cc_start: 0.4715 (mtp) cc_final: 0.4373 (ptm) REVERT: L 358 MET cc_start: 0.8722 (mmt) cc_final: 0.8492 (mmt) REVERT: N 260 MET cc_start: 0.8701 (ptm) cc_final: 0.8098 (ttm) REVERT: N 592 MET cc_start: 0.0639 (mmm) cc_final: 0.0428 (mmm) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.1784 time to fit residues: 43.8258 Evaluate side-chains 117 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 243 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 145 optimal weight: 6.9990 chunk 315 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 303 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 297 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 161 optimal weight: 20.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 GLN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 464 GLN ** M 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 276 GLN N 394 GLN N 505 ASN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN ** N 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.062212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.037377 restraints weight = 303298.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.037975 restraints weight = 255988.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.038337 restraints weight = 226500.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.038478 restraints weight = 209262.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.038753 restraints weight = 201339.019| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32305 Z= 0.201 Angle : 0.701 9.490 44902 Z= 0.384 Chirality : 0.043 0.229 5058 Planarity : 0.005 0.071 4730 Dihedral : 26.228 173.585 6580 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.04 % Allowed : 0.47 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.15), residues: 3088 helix: 0.08 (0.13), residues: 1611 sheet: -2.38 (0.32), residues: 239 loop : -1.92 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 39 TYR 0.032 0.002 TYR K 276 PHE 0.017 0.002 PHE L 475 TRP 0.022 0.002 TRP N 391 HIS 0.009 0.001 HIS M 419 Details of bonding type rmsd covalent geometry : bond 0.00434 (32302) covalent geometry : angle 0.70069 (44900) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.29250 ( 2) hydrogen bonds : bond 0.07220 ( 1470) hydrogen bonds : angle 4.76482 ( 4011) metal coordination : bond 0.00052 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9656.84 seconds wall clock time: 166 minutes 2.69 seconds (9962.69 seconds total)