Starting phenix.real_space_refine on Mon Sep 14 13:55:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6z6p_11102/09_2026/6z6p_11102.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z6p_11102/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6z6p_11102/09_2026/6z6p_11102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z6p_11102/09_2026/6z6p_11102.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6z6p_11102/09_2026/6z6p_11102.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6z6p_11102/09_2026/6z6p_11102.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6z6p_11102/09_2026/6z6p_11102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z6p_11102/09_2026/6z6p_11102.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 6.41, per 1000 atoms: 0.21 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: 2.37 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: 4.56 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: 6.99 Time building geometry restraints manager: 3.27 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=" C3' DA J -55 " pdb=" O3' DA J -55 " ideal model delta sigma weight residual 1.435 1.327 0.108 1.30e-02 5.92e+03 6.86e+01 bond pdb=" C5' DG J 20 " pdb=" C4' DG J 20 " ideal model delta sigma weight residual 1.512 1.562 -0.050 7.00e-03 2.04e+04 5.05e+01 bond pdb=" C3' DG J 20 " pdb=" C2' DG J 20 " ideal model delta sigma weight residual 1.516 1.568 -0.052 8.00e-03 1.56e+04 4.28e+01 bond pdb=" C5' DA I 39 " pdb=" C4' DA I 39 " ideal model delta sigma weight residual 1.512 1.557 -0.045 7.00e-03 2.04e+04 4.11e+01 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 ... (remaining 32297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 42824 3.55 - 7.10: 1795 7.10 - 10.65: 229 10.65 - 14.20: 39 14.20 - 17.75: 13 Bond angle restraints: 44900 Sorted by residual: angle pdb=" O4' DA I -35 " pdb=" C1' DA I -35 " pdb=" N9 DA I -35 " ideal model delta sigma weight residual 108.00 99.75 8.25 7.00e-01 2.04e+00 1.39e+02 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=" O4' DT J -63 " pdb=" C1' DT J -63 " pdb=" N1 DT J -63 " ideal model delta sigma weight residual 108.00 114.38 -6.38 7.00e-01 2.04e+00 8.30e+01 angle pdb=" C3' DG I -53 " pdb=" O3' DG I -53 " pdb=" P DG I -52 " ideal model delta sigma weight residual 119.70 129.88 -10.18 1.20e+00 6.94e-01 7.20e+01 angle pdb=" O4' DG I -49 " pdb=" C1' DG I -49 " pdb=" N9 DG I -49 " ideal model delta sigma weight residual 108.00 113.88 -5.88 7.00e-01 2.04e+00 7.06e+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: 4063 0.106 - 0.213: 848 0.213 - 0.319: 122 0.319 - 0.425: 20 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: 15.680 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 35.920 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 0.108 32305 Z= 0.714 Angle : 1.650 17.750 44902 Z= 1.017 Chirality : 0.088 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/Z covalent geometry : bond 0.00969 / 0.71 (32302) covalent geometry : angle 1.64989 / 1.02 (44900) SS BOND : bond 0.00399 / 0.21 ( 1) SS BOND : angle 0.31140 / 0.17 ( 2) hydrogen bonds : bond 0.17336 / 11.97 ( 1470) hydrogen bonds : angle 7.92677 / 5.59 ( 4011) metal coordination : bond 0.06946 / 3.64 ( 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 : 1.134 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: K 193 VAL cc_start: 0.6366 (m) cc_final: 0.6139 (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: 0.3040 (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: 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: 0.8980 (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: 5 residues processed: 263 average time/residue: 0.2174 time to fit residues: 90.6973 Evaluate side-chains 155 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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: 5.9990 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... K 41 GLN K 52 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** K 645 ASN L 69 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 454 ASN L 620 ASN ** L 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 682 ASN M 47 GLN M 112 ASN M 124 ASN M 258 ASN M 316 GLN M 409 ASN M 477 ASN M 572 ASN N 121 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 C 89 ASN 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: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.066754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.040833 restraints weight = 283546.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.041722 restraints weight = 221239.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.042299 restraints weight = 187828.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.042553 restraints weight = 168837.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.042553 restraints weight = 158478.234| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32305 Z= 0.205 Angle : 0.871 10.692 44902 Z= 0.468 Chirality : 0.054 0.372 5058 Planarity : 0.006 0.094 4730 Dihedral : 27.013 161.841 6580 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.18 % Allowed : 3.94 % Favored : 95.88 % 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: -3.37 (0.13), residues: 3088 helix: -1.80 (0.11), residues: 1595 sheet: -2.32 (0.32), residues: 213 loop : -2.69 (0.15), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 238 TYR 0.031 0.002 TYR H 39 PHE 0.033 0.002 PHE K 643 TRP 0.013 0.002 TRP L 428 HIS 0.011 0.001 HIS L 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.21 (32302) covalent geometry : angle 0.87127 / 0.47 (44900) SS BOND : bond 0.00177 / 0.09 ( 1) SS BOND : angle 0.42524 / 0.24 ( 2) hydrogen bonds : bond 0.08327 / 5.82 ( 1470) hydrogen bonds : angle 5.82123 / 4.12 ( 4011) metal coordination : bond 0.00749 / 0.39 ( 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 177 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 172 time to evaluate : 1.114 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: K 358 MET cc_start: 0.9386 (mtm) cc_final: 0.9101 (mtm) REVERT: L 66 MET cc_start: 0.6995 (mtm) cc_final: 0.6785 (mtm) REVERT: L 107 THR cc_start: 0.6843 (p) cc_final: 0.6621 (t) REVERT: N 92 VAL cc_start: 0.7147 (OUTLIER) cc_final: 0.6872 (p) REVERT: N 260 MET cc_start: 0.8790 (ptm) cc_final: 0.8360 (ttp) REVERT: N 394 GLN cc_start: 0.9098 (mm110) cc_final: 0.8864 (pp30) REVERT: N 592 MET cc_start: 0.2772 (tpt) cc_final: 0.2516 (tpt) REVERT: D 59 MET cc_start: 0.9898 (mmm) cc_final: 0.9605 (tpp) REVERT: D 97 LEU cc_start: 0.8197 (mt) cc_final: 0.7864 (mt) REVERT: G 72 ASP cc_start: 0.9006 (p0) cc_final: 0.8738 (p0) REVERT: H 98 LEU cc_start: 0.9263 (tp) cc_final: 0.9056 (tt) outliers start: 5 outliers final: 1 residues processed: 176 average time/residue: 0.2037 time to fit residues: 59.0051 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 : 1.125 ------------------------------------------------------------------------------- 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: 9.9990 chunk 281 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 301 optimal weight: 0.0570 chunk 89 optimal weight: 0.0870 chunk 203 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 chunk 108 optimal weight: 1.9990 chunk 277 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 overall best weight: 3.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 41 GLN K 100 ASN 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 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 HIS ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 369 ASN ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 ASN N 505 ASN ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 634 ASN ** A 68 GLN ** 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 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.077325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.057443 restraints weight = 383282.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.057853 restraints weight = 314399.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.058452 restraints weight = 270051.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.058498 restraints weight = 255553.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.058548 restraints weight = 231832.070| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32305 Z= 0.196 Angle : 0.816 12.329 44902 Z= 0.437 Chirality : 0.052 0.376 5058 Planarity : 0.006 0.093 4730 Dihedral : 26.754 164.420 6580 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.11 % Allowed : 4.72 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 1.63 % Twisted General : 0.07 % 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: -2.61 (0.14), residues: 3088 helix: -1.03 (0.12), residues: 1591 sheet: -2.35 (0.32), residues: 207 loop : -2.45 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 77 TYR 0.037 0.002 TYR L 583 PHE 0.029 0.002 PHE K 315 TRP 0.012 0.002 TRP L 540 HIS 0.008 0.001 HIS M 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.20 (32302) covalent geometry : angle 0.81597 / 0.44 (44900) SS BOND : bond 0.00215 / 0.11 ( 1) SS BOND : angle 0.33496 / 0.19 ( 2) hydrogen bonds : bond 0.08380 / 5.80 ( 1470) hydrogen bonds : angle 5.42097 / 3.84 ( 4011) metal coordination : bond 0.00196 / 0.10 ( 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 156 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.936 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: K 312 MET cc_start: 0.9458 (mmp) cc_final: 0.9249 (mmm) REVERT: L 107 THR cc_start: 0.7260 (p) cc_final: 0.6988 (t) REVERT: L 149 MET cc_start: 0.5380 (mtp) cc_final: 0.5040 (ptp) REVERT: L 329 ASP cc_start: 0.8585 (m-30) cc_final: 0.8344 (m-30) REVERT: L 358 MET cc_start: 0.8941 (mpp) cc_final: 0.8732 (mpp) REVERT: N 260 MET cc_start: 0.9296 (ptm) cc_final: 0.8873 (ttp) REVERT: N 394 GLN cc_start: 0.9146 (mm110) cc_final: 0.8934 (pt0) REVERT: N 592 MET cc_start: 0.2628 (tpt) cc_final: 0.2353 (tpt) REVERT: D 59 MET cc_start: 0.9882 (mmm) cc_final: 0.9621 (tpp) outliers start: 3 outliers final: 1 residues processed: 155 average time/residue: 0.1933 time to fit residues: 48.9166 Evaluate side-chains 117 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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: 3.9990 chunk 326 optimal weight: 30.0000 chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 290 optimal weight: 30.0000 chunk 221 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 205 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 507 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 454 ASN L 579 ASN ** L 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS M 112 ASN ** M 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 20 GLN N 281 ASN ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 505 ASN N 524 ASN ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 634 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.074870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.054404 restraints weight = 390165.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.054725 restraints weight = 334517.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.055047 restraints weight = 283078.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.055450 restraints weight = 254195.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.055560 restraints weight = 236425.645| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 32305 Z= 0.250 Angle : 0.849 13.186 44902 Z= 0.456 Chirality : 0.052 0.357 5058 Planarity : 0.006 0.079 4730 Dihedral : 26.731 166.813 6580 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 27.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.11 % Allowed : 4.94 % Favored : 94.95 % 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: -2.44 (0.14), residues: 3088 helix: -0.90 (0.12), residues: 1599 sheet: -2.47 (0.32), residues: 214 loop : -2.33 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 568 TYR 0.036 0.003 TYR F 88 PHE 0.032 0.003 PHE K 649 TRP 0.028 0.003 TRP M 32 HIS 0.014 0.002 HIS L 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.25 (32302) covalent geometry : angle 0.84892 / 0.46 (44900) SS BOND : bond 0.00213 / 0.11 ( 1) SS BOND : angle 0.34114 / 0.18 ( 2) hydrogen bonds : bond 0.10268 / 7.04 ( 1470) hydrogen bonds : angle 5.42507 / 3.82 ( 4011) metal coordination : bond 0.00075 / 0.04 ( 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 149 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 1.085 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: K 128 SER cc_start: 0.8835 (p) cc_final: 0.8561 (p) REVERT: K 358 MET cc_start: 0.8965 (mtt) cc_final: 0.8491 (mtt) REVERT: L 107 THR cc_start: 0.8140 (p) cc_final: 0.7846 (t) REVERT: L 149 MET cc_start: 0.5277 (mtp) cc_final: 0.4924 (ptm) REVERT: N 394 GLN cc_start: 0.9163 (mm110) cc_final: 0.8960 (pt0) REVERT: D 59 MET cc_start: 0.9905 (mmm) cc_final: 0.9670 (tpp) REVERT: E 73 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7782 (mt-10) outliers start: 3 outliers final: 1 residues processed: 148 average time/residue: 0.1815 time to fit residues: 45.2736 Evaluate side-chains 117 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 0.0060 chunk 50 optimal weight: 0.8980 chunk 188 optimal weight: 40.0000 chunk 53 optimal weight: 7.9990 chunk 295 optimal weight: 0.8980 chunk 265 optimal weight: 0.0070 chunk 315 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.1616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 41 GLN ** K 83 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 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 GLN L 443 ASN ** M 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 505 ASN ** N 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN N 634 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.077594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.057167 restraints weight = 381349.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.057993 restraints weight = 314144.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.058082 restraints weight = 257404.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.058380 restraints weight = 229163.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.058381 restraints weight = 211708.957| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32305 Z= 0.145 Angle : 0.745 10.398 44902 Z= 0.397 Chirality : 0.050 0.356 5058 Planarity : 0.005 0.080 4730 Dihedral : 26.620 167.148 6580 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.07 % Allowed : 2.58 % Favored : 97.35 % 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: -1.94 (0.14), residues: 3088 helix: -0.44 (0.12), residues: 1599 sheet: -2.21 (0.33), residues: 218 loop : -2.16 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 39 TYR 0.044 0.002 TYR N 571 PHE 0.032 0.002 PHE N 37 TRP 0.019 0.002 TRP L 428 HIS 0.008 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (32302) covalent geometry : angle 0.74525 / 0.40 (44900) SS BOND : bond 0.00135 / 0.07 ( 1) SS BOND : angle 0.32716 / 0.18 ( 2) hydrogen bonds : bond 0.06812 / 4.74 ( 1470) hydrogen bonds : angle 4.97234 / 3.51 ( 4011) metal coordination : bond 0.00086 / 0.04 ( 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 151 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 1.155 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 312 MET cc_start: 0.9527 (mmp) cc_final: 0.9221 (mmm) REVERT: K 358 MET cc_start: 0.8861 (mtt) cc_final: 0.8564 (mtt) REVERT: L 107 THR cc_start: 0.8265 (p) cc_final: 0.7917 (t) REVERT: L 149 MET cc_start: 0.5145 (mtp) cc_final: 0.4765 (ptm) REVERT: N 103 MET cc_start: 0.6177 (mmp) cc_final: 0.5767 (mtm) REVERT: N 394 GLN cc_start: 0.9203 (mm110) cc_final: 0.8947 (pt0) REVERT: N 592 MET cc_start: 0.2894 (tpt) cc_final: 0.2600 (tpt) REVERT: N 634 ASN cc_start: 0.6101 (OUTLIER) cc_final: 0.5899 (t0) REVERT: D 56 MET cc_start: 0.9332 (tpt) cc_final: 0.8841 (ptp) REVERT: E 73 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7706 (mt-10) REVERT: E 87 SER cc_start: 0.7341 (m) cc_final: 0.6911 (m) REVERT: F 84 MET cc_start: 0.9277 (mmp) cc_final: 0.9012 (tpp) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.1839 time to fit residues: 47.0777 Evaluate side-chains 119 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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: 9.9990 chunk 293 optimal weight: 1.9990 chunk 314 optimal weight: 30.0000 chunk 25 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 20.0000 chunk 298 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 488 ASN N 505 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** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.063308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.038432 restraints weight = 290924.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.038928 restraints weight = 249121.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.039336 restraints weight = 225086.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.039459 restraints weight = 208831.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.039678 restraints weight = 201366.708| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32305 Z= 0.188 Angle : 0.749 9.546 44902 Z= 0.403 Chirality : 0.049 0.339 5058 Planarity : 0.005 0.077 4730 Dihedral : 26.418 171.467 6580 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -1.84 (0.15), residues: 3088 helix: -0.34 (0.12), residues: 1608 sheet: -2.19 (0.33), residues: 219 loop : -2.15 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 39 TYR 0.035 0.002 TYR C 50 PHE 0.020 0.002 PHE K 315 TRP 0.017 0.002 TRP K 428 HIS 0.009 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 (32302) covalent geometry : angle 0.74853 / 0.40 (44900) SS BOND : bond 0.00155 / 0.08 ( 1) SS BOND : angle 0.28686 / 0.15 ( 2) hydrogen bonds : bond 0.08418 / 5.77 ( 1470) hydrogen bonds : angle 5.00420 / 3.52 ( 4011) metal coordination : bond 0.00155 / 0.07 ( 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 143 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.005 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: 0.9550 (mmp) cc_final: 0.9239 (mmm) REVERT: K 358 MET cc_start: 0.9225 (mtt) cc_final: 0.8871 (mtt) REVERT: L 107 THR cc_start: 0.7355 (p) cc_final: 0.7087 (t) REVERT: L 149 MET cc_start: 0.5165 (mtp) cc_final: 0.4873 (ptm) REVERT: N 103 MET cc_start: 0.6208 (mmp) cc_final: 0.5869 (mtp) REVERT: N 260 MET cc_start: 0.8953 (ptm) cc_final: 0.8416 (ttm) REVERT: N 394 GLN cc_start: 0.9229 (mm110) cc_final: 0.8977 (pt0) REVERT: N 592 MET cc_start: 0.3287 (tpt) cc_final: 0.3039 (tpt) REVERT: D 59 MET cc_start: 0.9930 (mmm) cc_final: 0.9694 (tpp) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1822 time to fit residues: 44.9816 Evaluate side-chains 115 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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: 0.0030 chunk 125 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 256 optimal weight: 9.9990 chunk 279 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 83 optimal weight: 0.0980 overall best weight: 4.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 GLN ** 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** ** M 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 505 ASN ** 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 82 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.062833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.038126 restraints weight = 294923.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.038643 restraints weight = 255021.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.038973 restraints weight = 229283.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.039316 restraints weight = 213741.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.039439 restraints weight = 201445.832| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32305 Z= 0.192 Angle : 0.748 9.395 44902 Z= 0.403 Chirality : 0.049 0.341 5058 Planarity : 0.005 0.077 4730 Dihedral : 26.465 178.190 6580 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.04 % Allowed : 1.54 % Favored : 98.43 % 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: -1.82 (0.15), residues: 3088 helix: -0.31 (0.12), residues: 1609 sheet: -2.33 (0.32), residues: 228 loop : -2.13 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 39 TYR 0.029 0.002 TYR C 50 PHE 0.029 0.002 PHE L 475 TRP 0.015 0.002 TRP M 298 HIS 0.025 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (32302) covalent geometry : angle 0.74764 / 0.40 (44900) SS BOND : bond 0.00200 / 0.11 ( 1) SS BOND : angle 0.30463 / 0.16 ( 2) hydrogen bonds : bond 0.08046 / 5.52 ( 1470) hydrogen bonds : angle 4.96462 / 3.49 ( 4011) metal coordination : bond 0.00069 / 0.03 ( 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 143 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 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: K 312 MET cc_start: 0.9550 (mmp) cc_final: 0.9239 (mmm) REVERT: K 358 MET cc_start: 0.9106 (mtt) cc_final: 0.8880 (mtt) REVERT: L 41 GLN cc_start: 0.5981 (OUTLIER) cc_final: 0.5466 (pp30) REVERT: L 107 THR cc_start: 0.7629 (p) cc_final: 0.7329 (t) REVERT: L 149 MET cc_start: 0.5123 (mtp) cc_final: 0.4805 (ptm) REVERT: M 284 LEU cc_start: -0.2099 (tp) cc_final: -0.2347 (tp) REVERT: N 260 MET cc_start: 0.8948 (ptm) cc_final: 0.8383 (ttm) REVERT: N 394 GLN cc_start: 0.9220 (mm110) cc_final: 0.8970 (pt0) REVERT: N 592 MET cc_start: 0.3285 (tpt) cc_final: 0.3033 (tpt) REVERT: D 59 MET cc_start: 0.9928 (mmm) cc_final: 0.9713 (tpp) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1841 time to fit residues: 45.1807 Evaluate side-chains 114 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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: 30.0000 chunk 323 optimal weight: 40.0000 chunk 120 optimal weight: 10.0000 chunk 320 optimal weight: 20.0000 chunk 329 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 309 optimal weight: 50.0000 chunk 275 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 41 GLN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 HIS ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 464 GLN ** M 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 505 ASN N 629 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.051142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.032832 restraints weight = 371965.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.033227 restraints weight = 306846.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.033374 restraints weight = 269008.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.033635 restraints weight = 251919.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.033827 restraints weight = 233500.466| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 32305 Z= 0.251 Angle : 0.824 10.461 44902 Z= 0.443 Chirality : 0.051 0.349 5058 Planarity : 0.006 0.076 4730 Dihedral : 26.601 157.692 6580 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 30.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -2.10 (0.14), residues: 3088 helix: -0.58 (0.12), residues: 1604 sheet: -2.47 (0.32), residues: 229 loop : -2.19 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG D 76 TYR 0.035 0.002 TYR K 276 PHE 0.027 0.003 PHE K 431 TRP 0.018 0.003 TRP L 540 HIS 0.016 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.25 (32302) covalent geometry : angle 0.82361 / 0.44 (44900) SS BOND : bond 0.00181 / 0.10 ( 1) SS BOND : angle 0.19303 / 0.10 ( 2) hydrogen bonds : bond 0.10325 / 7.05 ( 1470) hydrogen bonds : angle 5.18382 / 3.63 ( 4011) metal coordination : bond 0.00138 / 0.07 ( 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 142 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.089 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: K 312 MET cc_start: 0.9513 (mmp) cc_final: 0.9257 (mmm) REVERT: L 107 THR cc_start: 0.7765 (p) cc_final: 0.7488 (t) REVERT: L 149 MET cc_start: 0.4964 (mtp) cc_final: 0.4617 (ptp) REVERT: L 473 PHE cc_start: 0.9092 (m-80) cc_final: 0.8875 (p90) REVERT: N 103 MET cc_start: 0.6199 (mmp) cc_final: 0.5765 (mtm) REVERT: N 260 MET cc_start: 0.8944 (ptm) cc_final: 0.8355 (ttm) REVERT: N 592 MET cc_start: 0.3375 (tpt) cc_final: 0.3141 (tpt) REVERT: A 70 LEU cc_start: 0.9620 (tt) cc_final: 0.9378 (mp) REVERT: D 59 MET cc_start: 0.9935 (mmm) cc_final: 0.9732 (tpp) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1855 time to fit residues: 44.8537 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 : 1.045 ------------------------------------------------------------------------------- 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: 10.0000 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 41 GLN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 293 HIS ** M 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 HIS ** 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.051071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.032789 restraints weight = 374452.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.033224 restraints weight = 308193.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.033439 restraints weight = 266825.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.033693 restraints weight = 244563.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.033693 restraints weight = 227241.547| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32305 Z= 0.241 Angle : 0.825 10.203 44902 Z= 0.445 Chirality : 0.052 0.381 5058 Planarity : 0.006 0.109 4730 Dihedral : 26.816 142.359 6580 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 31.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: -2.18 (0.14), residues: 3088 helix: -0.62 (0.12), residues: 1596 sheet: -2.55 (0.32), residues: 228 loop : -2.25 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 39 TYR 0.035 0.002 TYR K 276 PHE 0.049 0.003 PHE E 104 TRP 0.052 0.003 TRP N 391 HIS 0.018 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.24 (32302) covalent geometry : angle 0.82521 / 0.45 (44900) SS BOND : bond 0.00066 / 0.03 ( 1) SS BOND : angle 0.38871 / 0.21 ( 2) hydrogen bonds : bond 0.09362 / 6.39 ( 1470) hydrogen bonds : angle 5.24444 / 3.66 ( 4011) metal coordination : bond 0.00123 / 0.06 ( 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 142 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.065 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 322 MET cc_start: 0.8717 (tpt) cc_final: 0.8444 (tpt) REVERT: L 107 THR cc_start: 0.7581 (p) cc_final: 0.7332 (t) REVERT: L 149 MET cc_start: 0.5025 (mtp) cc_final: 0.4682 (ptp) REVERT: L 358 MET cc_start: 0.8717 (mmt) cc_final: 0.8484 (mmt) REVERT: N 260 MET cc_start: 0.8769 (ptm) cc_final: 0.8134 (ttm) REVERT: N 592 MET cc_start: 0.3475 (tpt) cc_final: 0.3230 (tpt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1896 time to fit residues: 45.0062 Evaluate side-chains 105 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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: 0.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 301 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 ASN ** 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 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 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 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 293 HIS ** M 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 576 ASN N 505 ASN N 629 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.051381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.032982 restraints weight = 371059.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.033403 restraints weight = 303670.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.033716 restraints weight = 266735.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.033867 restraints weight = 242262.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.034044 restraints weight = 226642.468| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32305 Z= 0.216 Angle : 0.806 10.188 44902 Z= 0.434 Chirality : 0.052 0.378 5058 Planarity : 0.005 0.075 4730 Dihedral : 26.798 146.162 6580 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 29.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -2.09 (0.14), residues: 3088 helix: -0.51 (0.12), residues: 1596 sheet: -2.60 (0.32), residues: 229 loop : -2.23 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 67 TYR 0.037 0.002 TYR K 276 PHE 0.028 0.002 PHE E 104 TRP 0.028 0.003 TRP N 391 HIS 0.016 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.22 (32302) covalent geometry : angle 0.80589 / 0.43 (44900) SS BOND : bond 0.00212 / 0.11 ( 1) SS BOND : angle 0.16726 / 0.09 ( 2) hydrogen bonds : bond 0.09005 / 6.16 ( 1470) hydrogen bonds : angle 5.18996 / 3.63 ( 4011) metal coordination : bond 0.00082 / 0.04 ( 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 142 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.183 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: K 312 MET cc_start: 0.9473 (mmm) cc_final: 0.9268 (mmm) REVERT: K 358 MET cc_start: 0.9357 (mtm) cc_final: 0.9134 (mtt) REVERT: L 107 THR cc_start: 0.7661 (p) cc_final: 0.7401 (t) REVERT: L 149 MET cc_start: 0.5012 (mtp) cc_final: 0.4668 (ptp) REVERT: L 358 MET cc_start: 0.8737 (mmt) cc_final: 0.8444 (mmt) REVERT: N 260 MET cc_start: 0.8829 (ptm) cc_final: 0.8227 (ttm) REVERT: N 592 MET cc_start: 0.3460 (tpt) cc_final: 0.3232 (tpt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1802 time to fit residues: 44.1394 Evaluate side-chains 110 residues out of total 2794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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: 2.9990 chunk 35 optimal weight: 0.0980 chunk 145 optimal weight: 5.9990 chunk 315 optimal weight: 30.0000 chunk 80 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 41 GLN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 467 HIS ** 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 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 290 GLN ** M 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 505 ASN N 629 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.062924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.037832 restraints weight = 298597.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.038403 restraints weight = 252819.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.038828 restraints weight = 226134.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.039060 restraints weight = 207860.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.039278 restraints weight = 194715.948| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32305 Z= 0.161 Angle : 0.756 9.439 44902 Z= 0.406 Chirality : 0.051 0.373 5058 Planarity : 0.005 0.074 4730 Dihedral : 26.706 148.509 6580 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -1.85 (0.15), residues: 3088 helix: -0.33 (0.12), residues: 1605 sheet: -2.56 (0.32), residues: 230 loop : -2.10 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 39 TYR 0.033 0.002 TYR K 276 PHE 0.032 0.002 PHE E 104 TRP 0.027 0.002 TRP N 391 HIS 0.013 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (32302) covalent geometry : angle 0.75563 / 0.41 (44900) SS BOND : bond 0.00139 / 0.07 ( 1) SS BOND : angle 0.27730 / 0.16 ( 2) hydrogen bonds : bond 0.07210 / 4.96 ( 1470) hydrogen bonds : angle 5.00800 / 3.51 ( 4011) metal coordination : bond 0.00026 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8780.00 seconds wall clock time: 151 minutes 40.01 seconds (9100.01 seconds total)