Starting phenix.real_space_refine on Mon Aug 25 13:26:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqf_37743/08_2025/8wqf_37743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqf_37743/08_2025/8wqf_37743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wqf_37743/08_2025/8wqf_37743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqf_37743/08_2025/8wqf_37743.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wqf_37743/08_2025/8wqf_37743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqf_37743/08_2025/8wqf_37743.map" } resolution = 3.27 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6261 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 169 5.16 5 C 14821 2.51 5 N 4033 2.21 5 O 4375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23404 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5953 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 706} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "H" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 618 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 5947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5947 Classifications: {'peptide': 725} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 705} Chain breaks: 1 Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "D" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "F" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2136 Classifications: {'peptide': 268} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 260} Chain: "J" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "E" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 703 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 71 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7735 SG CYS I 53 96.180 66.306 98.529 1.00 23.84 S ATOM 7758 SG CYS I 56 93.068 65.305 96.237 1.00 17.73 S ATOM 7786 SG CYS I 68 93.590 63.847 99.756 1.00 30.16 S ATOM 7649 SG CYS I 42 99.194 66.213 105.267 1.00 38.16 S ATOM 7668 SG CYS I 45 98.261 69.421 103.358 1.00 32.99 S ATOM 7904 SG CYS I 83 99.972 66.590 101.488 1.00 20.49 S ATOM 7836 SG CYS I 75 105.931 57.685 112.499 1.00 39.58 S ATOM 8000 SG CYS I 94 108.273 58.823 109.969 1.00 58.18 S ATOM 22898 SG CYS E 53 113.235 126.332 97.154 1.00 24.81 S ATOM 22921 SG CYS E 56 116.982 126.599 96.289 1.00 37.02 S ATOM 23005 SG CYS E 68 114.771 124.064 94.460 1.00 31.10 S ATOM 22812 SG CYS E 42 106.005 123.182 96.884 1.00 30.88 S ATOM 22831 SG CYS E 45 106.992 126.849 96.548 1.00 16.59 S ATOM 23123 SG CYS E 83 109.111 124.628 98.656 1.00 31.24 S ATOM 23055 SG CYS E 75 100.165 112.599 100.186 1.00 27.05 S ATOM 23219 SG CYS E 94 100.864 116.014 101.906 1.00 1.30 S Time building chain proxies: 6.11, per 1000 atoms: 0.26 Number of scatterers: 23404 At special positions: 0 Unit cell: (132.02, 176.3, 177.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 169 16.00 O 4375 8.00 N 4033 7.00 C 14821 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 200 " pdb="ZN ZN E 200 " - pdb=" ND1 HIS E 82 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 68 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 56 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 53 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 80 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 45 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 83 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 42 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 94 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 75 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 77 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" ND1 HIS I 82 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 68 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 53 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 56 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 80 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 45 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 83 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 94 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 77 " Number of angles added : 12 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5604 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 14 sheets defined 61.1% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 9 through 25 removed outlier: 3.811A pdb=" N THR A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 48 Processing helix chain 'A' and resid 53 through 79 removed outlier: 3.536A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 removed outlier: 3.715A pdb=" N GLU A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.873A pdb=" N ASP A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.603A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.683A pdb=" N ARG A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.752A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 207 through 228 removed outlier: 3.848A pdb=" N GLN A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.947A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 271 removed outlier: 3.755A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.685A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 307 through 327 removed outlier: 4.154A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 357 removed outlier: 3.528A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 Processing helix chain 'A' and resid 386 through 400 removed outlier: 3.603A pdb=" N CYS A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 423 removed outlier: 3.826A pdb=" N ASP A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 445 removed outlier: 3.756A pdb=" N HIS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 471 through 497 removed outlier: 3.668A pdb=" N MET A 480 " --> pdb=" O MET A 476 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 548 removed outlier: 4.078A pdb=" N LYS A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N SER A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 removed outlier: 4.321A pdb=" N VAL A 584 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 585 " --> pdb=" O GLN A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 603 Processing helix chain 'A' and resid 606 through 620 removed outlier: 3.525A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 692 removed outlier: 3.801A pdb=" N ASP A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 removed outlier: 3.747A pdb=" N GLN A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 728 removed outlier: 3.671A pdb=" N ILE A 726 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 37 Processing helix chain 'G' and resid 39 through 47 removed outlier: 3.823A pdb=" N LYS G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 83 Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'H' and resid 23 through 36 removed outlier: 4.301A pdb=" N LEU H 27 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE H 34 " --> pdb=" O ILE H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 61 removed outlier: 3.510A pdb=" N GLY H 61 " --> pdb=" O GLY H 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 91 Processing helix chain 'B' and resid 9 through 26 Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.669A pdb=" N SER B 40 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 79 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 155 through 172 removed outlier: 3.537A pdb=" N LEU B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 removed outlier: 4.078A pdb=" N PHE B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 207 through 230 Processing helix chain 'B' and resid 231 through 252 removed outlier: 3.757A pdb=" N GLU B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 258 through 271 removed outlier: 3.557A pdb=" N ILE B 263 " --> pdb=" O TYR B 259 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 270 " --> pdb=" O CYS B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.627A pdb=" N LEU B 278 " --> pdb=" O HIS B 274 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU B 281 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N HIS B 283 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 304 removed outlier: 4.194A pdb=" N ALA B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 327 removed outlier: 4.150A pdb=" N MET B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 357 removed outlier: 3.648A pdb=" N VAL B 340 " --> pdb=" O PRO B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 377 removed outlier: 3.691A pdb=" N SER B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 400 Processing helix chain 'B' and resid 407 through 423 removed outlier: 3.660A pdb=" N ILE B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 445 removed outlier: 3.639A pdb=" N LYS B 441 " --> pdb=" O ARG B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 466 Processing helix chain 'B' and resid 472 through 482 removed outlier: 3.589A pdb=" N MET B 480 " --> pdb=" O MET B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 496 Processing helix chain 'B' and resid 530 through 548 removed outlier: 4.066A pdb=" N LYS B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER B 536 " --> pdb=" O GLU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 570 removed outlier: 3.869A pdb=" N GLY B 570 " --> pdb=" O ASN B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 567 through 570' Processing helix chain 'B' and resid 579 through 589 removed outlier: 3.584A pdb=" N VAL B 584 " --> pdb=" O TYR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 603 Processing helix chain 'B' and resid 606 through 621 Processing helix chain 'B' and resid 661 through 691 Processing helix chain 'B' and resid 695 through 708 Processing helix chain 'B' and resid 714 through 728 Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 46 Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.741A pdb=" N ALA C 53 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C 54 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 83 Processing helix chain 'C' and resid 102 through 110 removed outlier: 3.517A pdb=" N ALA C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.700A pdb=" N LEU D 27 " --> pdb=" O THR D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'F' and resid 361 through 377 Processing helix chain 'F' and resid 381 through 398 Processing helix chain 'F' and resid 404 through 427 removed outlier: 4.225A pdb=" N ASN F 427 " --> pdb=" O ASN F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 457 Processing helix chain 'F' and resid 460 through 478 Processing helix chain 'F' and resid 486 through 492 Processing helix chain 'F' and resid 502 through 507 removed outlier: 4.060A pdb=" N VAL F 506 " --> pdb=" O HIS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 521 removed outlier: 3.571A pdb=" N LYS F 516 " --> pdb=" O ALA F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 540 removed outlier: 3.839A pdb=" N ILE F 539 " --> pdb=" O ALA F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 562 removed outlier: 3.587A pdb=" N ILE F 556 " --> pdb=" O LEU F 552 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER F 558 " --> pdb=" O SER F 554 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU F 561 " --> pdb=" O ILE F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 593 removed outlier: 3.557A pdb=" N GLU F 586 " --> pdb=" O THR F 582 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN F 592 " --> pdb=" O LEU F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 608 Processing helix chain 'F' and resid 617 through 622 removed outlier: 3.777A pdb=" N GLU F 622 " --> pdb=" O ARG F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 627 Processing helix chain 'J' and resid 2 through 15 Processing helix chain 'J' and resid 17 through 24 Processing helix chain 'J' and resid 28 through 37 Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 58 through 68 removed outlier: 4.140A pdb=" N VAL J 62 " --> pdb=" O HIS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 99 Processing helix chain 'J' and resid 100 through 110 Processing helix chain 'J' and resid 124 through 132 Processing helix chain 'J' and resid 133 through 143 removed outlier: 4.042A pdb=" N VAL J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 164 Processing helix chain 'J' and resid 167 through 175 Processing helix chain 'J' and resid 190 through 198 removed outlier: 4.045A pdb=" N GLU J 196 " --> pdb=" O HIS J 192 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA J 197 " --> pdb=" O PHE J 193 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 209 Processing helix chain 'J' and resid 221 through 229 Processing helix chain 'J' and resid 231 through 239 Processing helix chain 'J' and resid 245 through 262 removed outlier: 3.586A pdb=" N ALA J 261 " --> pdb=" O GLY J 257 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN J 262 " --> pdb=" O ALA J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 284 Processing helix chain 'J' and resid 310 through 317 Processing helix chain 'J' and resid 320 through 337 Processing helix chain 'J' and resid 344 through 357 Processing helix chain 'J' and resid 360 through 377 Processing helix chain 'J' and resid 383 through 398 Processing helix chain 'J' and resid 403 through 428 Processing helix chain 'J' and resid 432 through 456 Processing helix chain 'J' and resid 460 through 476 Processing helix chain 'J' and resid 489 through 493 Processing helix chain 'J' and resid 502 through 507 removed outlier: 4.098A pdb=" N VAL J 506 " --> pdb=" O HIS J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 511 through 521 Processing helix chain 'J' and resid 535 through 540 removed outlier: 3.918A pdb=" N ILE J 539 " --> pdb=" O ALA J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 562 Processing helix chain 'J' and resid 582 through 593 Processing helix chain 'J' and resid 596 through 608 Processing helix chain 'J' and resid 617 through 626 removed outlier: 3.834A pdb=" N GLU J 622 " --> pdb=" O ARG J 618 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE J 623 " --> pdb=" O THR J 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 89 Processing helix chain 'K' and resid -22 through -18 removed outlier: 3.679A pdb=" N LEU K -18 " --> pdb=" O PHE K -22 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid -22 through -18' Processing helix chain 'K' and resid -17 through -15 No H-bonds generated for 'chain 'K' and resid -17 through -15' Processing sheet with id=AA1, first strand: chain 'A' and resid 507 through 513 removed outlier: 4.732A pdb=" N VAL I 30 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 561 through 564 removed outlier: 4.370A pdb=" N ALA A 575 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA4, first strand: chain 'A' and resid 694 through 695 Processing sheet with id=AA5, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AA6, first strand: chain 'H' and resid 13 through 18 Processing sheet with id=AA7, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AA8, first strand: chain 'B' and resid 510 through 513 removed outlier: 6.043A pdb=" N TYR B 510 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TRP E 33 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B 512 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N TRP E 35 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N VAL E 24 " --> pdb=" O GLY B 562 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N GLY B 562 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N LYS E 26 " --> pdb=" O CYS B 560 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N CYS B 560 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 11.391A pdb=" N ASN E 28 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N TYR B 558 " --> pdb=" O ASN E 28 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL E 30 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 623 through 625 Processing sheet with id=AB1, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AB2, first strand: chain 'C' and resid 60 through 61 removed outlier: 4.861A pdb=" N LYS C 32 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N ASP D 17 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 73 " --> pdb=" O PHE D 4 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 40 through 42 Processing sheet with id=AB4, first strand: chain 'J' and resid 78 through 80 removed outlier: 7.484A pdb=" N ILE J 86 " --> pdb=" O VAL J 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 70 through 72 1235 hydrogen bonds defined for protein. 3648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.01 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7692 1.34 - 1.46: 4045 1.46 - 1.58: 11854 1.58 - 1.69: 0 1.69 - 1.81: 265 Bond restraints: 23856 Sorted by residual: bond pdb=" C ALA B 522 " pdb=" N PRO B 523 " ideal model delta sigma weight residual 1.339 1.392 -0.053 3.40e-02 8.65e+02 2.45e+00 bond pdb=" CG LEU G 70 " pdb=" CD2 LEU G 70 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.20e+00 bond pdb=" CD2 PHE F 392 " pdb=" CE2 PHE F 392 " ideal model delta sigma weight residual 1.382 1.338 0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CG1 ILE J 453 " pdb=" CD1 ILE J 453 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.88e+00 bond pdb=" CG LEU J 620 " pdb=" CD1 LEU J 620 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 ... (remaining 23851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 31977 2.62 - 5.24: 221 5.24 - 7.86: 26 7.86 - 10.48: 0 10.48 - 13.10: 3 Bond angle restraints: 32227 Sorted by residual: angle pdb=" CA LEU B 155 " pdb=" CB LEU B 155 " pdb=" CG LEU B 155 " ideal model delta sigma weight residual 116.30 129.40 -13.10 3.50e+00 8.16e-02 1.40e+01 angle pdb=" C HIS J 241 " pdb=" N ALA J 242 " pdb=" CA ALA J 242 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N PHE A 711 " pdb=" CA PHE A 711 " pdb=" C PHE A 711 " ideal model delta sigma weight residual 110.24 114.52 -4.28 1.30e+00 5.92e-01 1.09e+01 angle pdb=" C THR J 189 " pdb=" N ALA J 190 " pdb=" CA ALA J 190 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C TYR J 84 " pdb=" N VAL J 85 " pdb=" CA VAL J 85 " ideal model delta sigma weight residual 121.97 127.49 -5.52 1.80e+00 3.09e-01 9.39e+00 ... (remaining 32222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 12856 17.66 - 35.33: 1386 35.33 - 52.99: 231 52.99 - 70.65: 41 70.65 - 88.31: 25 Dihedral angle restraints: 14539 sinusoidal: 5941 harmonic: 8598 Sorted by residual: dihedral pdb=" CA VAL B 357 " pdb=" C VAL B 357 " pdb=" N LEU B 358 " pdb=" CA LEU B 358 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ASN B 359 " pdb=" C ASN B 359 " pdb=" N GLY B 360 " pdb=" CA GLY B 360 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TYR B 424 " pdb=" C TYR B 424 " pdb=" N ILE B 425 " pdb=" CA ILE B 425 " ideal model delta harmonic sigma weight residual -180.00 -159.55 -20.45 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 14536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2768 0.047 - 0.093: 686 0.093 - 0.140: 153 0.140 - 0.186: 10 0.186 - 0.233: 1 Chirality restraints: 3618 Sorted by residual: chirality pdb=" CB THR B 655 " pdb=" CA THR B 655 " pdb=" OG1 THR B 655 " pdb=" CG2 THR B 655 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB VAL A 191 " pdb=" CA VAL A 191 " pdb=" CG1 VAL A 191 " pdb=" CG2 VAL A 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CB VAL C 73 " pdb=" CA VAL C 73 " pdb=" CG1 VAL C 73 " pdb=" CG2 VAL C 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.17e-01 ... (remaining 3615 not shown) Planarity restraints: 4130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 388 " -0.020 2.00e-02 2.50e+03 2.16e-02 8.14e+00 pdb=" CG PHE F 388 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE F 388 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE F 388 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 388 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 388 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 388 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 510 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C TYR B 510 " -0.034 2.00e-02 2.50e+03 pdb=" O TYR B 510 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 511 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 65 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO C 66 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 66 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 66 " -0.025 5.00e-02 4.00e+02 ... (remaining 4127 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1949 2.74 - 3.28: 24054 3.28 - 3.82: 39813 3.82 - 4.36: 47064 4.36 - 4.90: 81905 Nonbonded interactions: 194785 Sorted by model distance: nonbonded pdb=" O ILE F 546 " pdb=" OH TYR J 275 " model vdw 2.199 3.040 nonbonded pdb=" OG SER J 393 " pdb=" O HIS J 502 " model vdw 2.219 3.040 nonbonded pdb=" OG SER F 393 " pdb=" O HIS F 502 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR J 302 " pdb=" OE1 GLU J 333 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR J 449 " pdb=" O PRO J 497 " model vdw 2.226 3.040 ... (remaining 194780 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 1 through 115 or resid 135 through 744)) selection = (chain 'B' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 744)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and (resid 22 through 59 or resid 68 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 104 or r \ esid 200 through 202)) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.580 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5480 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 : 0.004 0.053 23878 Z= 0.176 Angle : 0.600 13.100 32239 Z= 0.315 Chirality : 0.042 0.233 3618 Planarity : 0.004 0.046 4130 Dihedral : 14.916 88.313 8935 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.15), residues: 2869 helix: 0.13 (0.12), residues: 1712 sheet: -1.68 (0.56), residues: 73 loop : -1.66 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 442 TYR 0.027 0.001 TYR J 542 PHE 0.049 0.002 PHE F 388 TRP 0.023 0.002 TRP A 35 HIS 0.005 0.001 HIS I 48 Details of bonding type rmsd covalent geometry : bond 0.00423 (23856) covalent geometry : angle 0.59818 (32227) hydrogen bonds : bond 0.13992 ( 1235) hydrogen bonds : angle 6.27184 ( 3648) metal coordination : bond 0.00818 ( 22) metal coordination : angle 2.48687 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.2760 (mtp) cc_final: 0.2528 (mtm) REVERT: A 409 ASN cc_start: 0.4768 (p0) cc_final: 0.4368 (t0) REVERT: A 455 GLU cc_start: 0.4687 (tt0) cc_final: 0.4402 (tp30) REVERT: A 468 GLU cc_start: 0.5940 (tm-30) cc_final: 0.5646 (tt0) REVERT: A 489 LYS cc_start: 0.4555 (mtpt) cc_final: 0.4221 (mtpt) REVERT: G 24 SER cc_start: 0.8015 (t) cc_final: 0.7361 (t) REVERT: I 50 MET cc_start: 0.4769 (mmt) cc_final: 0.1853 (ptm) REVERT: B 206 ILE cc_start: 0.3595 (mm) cc_final: 0.3378 (mm) REVERT: B 253 TYR cc_start: 0.0352 (m-10) cc_final: 0.0080 (m-10) REVERT: B 271 VAL cc_start: 0.0957 (p) cc_final: 0.0401 (t) REVERT: B 567 ASN cc_start: 0.7828 (p0) cc_final: 0.7141 (t0) REVERT: D 43 ARG cc_start: 0.7358 (tpm170) cc_final: 0.7143 (tpt90) REVERT: D 53 ASP cc_start: 0.7397 (m-30) cc_final: 0.6731 (t70) REVERT: F 408 GLU cc_start: 0.6549 (pt0) cc_final: 0.6285 (mt-10) REVERT: F 530 ASN cc_start: 0.7475 (m-40) cc_final: 0.7170 (m-40) REVERT: F 567 ASP cc_start: 0.8566 (t70) cc_final: 0.8265 (t0) REVERT: F 615 GLN cc_start: 0.7859 (mp10) cc_final: 0.7444 (mp10) REVERT: J 437 MET cc_start: 0.7570 (tpt) cc_final: 0.7142 (tpt) REVERT: J 567 ASP cc_start: 0.7731 (t0) cc_final: 0.7304 (t70) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1820 time to fit residues: 123.8523 Evaluate side-chains 302 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 274 HIS A 513 GLN H 42 GLN I 28 ASN ** I 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 ASN F 476 HIS F 511 ASN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 ASN ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 511 ASN E 59 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.207806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.168641 restraints weight = 28896.417| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.63 r_work: 0.3773 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23878 Z= 0.161 Angle : 0.570 13.332 32239 Z= 0.299 Chirality : 0.040 0.183 3618 Planarity : 0.004 0.062 4130 Dihedral : 4.286 36.530 3140 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.89 % Allowed : 7.55 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.16), residues: 2869 helix: 0.52 (0.13), residues: 1737 sheet: -1.54 (0.58), residues: 64 loop : -1.57 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 374 TYR 0.022 0.001 TYR J 472 PHE 0.032 0.001 PHE J 501 TRP 0.024 0.002 TRP J 209 HIS 0.010 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00375 (23856) covalent geometry : angle 0.56879 (32227) hydrogen bonds : bond 0.04423 ( 1235) hydrogen bonds : angle 4.94461 ( 3648) metal coordination : bond 0.00738 ( 22) metal coordination : angle 2.29127 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 335 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7488 (ptpt) cc_final: 0.7273 (tppt) REVERT: A 413 ASP cc_start: 0.7831 (t70) cc_final: 0.7441 (t0) REVERT: A 476 MET cc_start: 0.9076 (ttm) cc_final: 0.8856 (mtp) REVERT: A 582 MET cc_start: 0.6515 (ptm) cc_final: 0.5877 (tmm) REVERT: I 50 MET cc_start: 0.4129 (mmt) cc_final: 0.0229 (ptm) REVERT: B 288 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7477 (mp10) REVERT: B 567 ASN cc_start: 0.7619 (p0) cc_final: 0.7304 (p0) REVERT: C 102 GLU cc_start: 0.7790 (tp30) cc_final: 0.7497 (tp30) REVERT: C 111 ASP cc_start: 0.8525 (t0) cc_final: 0.8314 (t0) REVERT: D 43 ARG cc_start: 0.7572 (tpm170) cc_final: 0.6841 (tpt170) REVERT: D 53 ASP cc_start: 0.7112 (m-30) cc_final: 0.6199 (t70) REVERT: F 408 GLU cc_start: 0.6736 (pt0) cc_final: 0.6451 (mt-10) REVERT: F 567 ASP cc_start: 0.8352 (t70) cc_final: 0.8071 (t0) REVERT: J 437 MET cc_start: 0.7490 (tpt) cc_final: 0.7113 (tpt) REVERT: J 567 ASP cc_start: 0.7585 (t0) cc_final: 0.7131 (t70) REVERT: E 36 ASP cc_start: 0.8419 (t0) cc_final: 0.7680 (t0) outliers start: 23 outliers final: 14 residues processed: 347 average time/residue: 0.1720 time to fit residues: 95.1302 Evaluate side-chains 314 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 299 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain J residue 186 CYS Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 465 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 133 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 277 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 210 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 228 GLN I 28 ASN I 48 HIS B 156 GLN ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 58 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.214281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.4071 r_free = 0.4071 target = 0.167791 restraints weight = 29822.904| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.23 r_work: 0.3843 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23878 Z= 0.162 Angle : 0.559 12.641 32239 Z= 0.292 Chirality : 0.040 0.254 3618 Planarity : 0.004 0.056 4130 Dihedral : 4.253 38.402 3140 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.50 % Allowed : 10.29 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2869 helix: 0.64 (0.13), residues: 1739 sheet: -1.88 (0.53), residues: 80 loop : -1.63 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 374 TYR 0.033 0.001 TYR B 510 PHE 0.035 0.002 PHE J 501 TRP 0.021 0.002 TRP J 209 HIS 0.016 0.001 HIS F 382 Details of bonding type rmsd covalent geometry : bond 0.00384 (23856) covalent geometry : angle 0.55783 (32227) hydrogen bonds : bond 0.03928 ( 1235) hydrogen bonds : angle 4.73196 ( 3648) metal coordination : bond 0.00732 ( 22) metal coordination : angle 2.09519 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 311 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7556 (ptpt) cc_final: 0.7308 (tppt) REVERT: A 582 MET cc_start: 0.6671 (ptm) cc_final: 0.6309 (tmm) REVERT: A 701 GLN cc_start: 0.7598 (tm-30) cc_final: 0.7397 (tm-30) REVERT: A 717 MET cc_start: 0.7737 (ttm) cc_final: 0.7451 (ttp) REVERT: I 50 MET cc_start: 0.4285 (mmt) cc_final: 0.0384 (ptm) REVERT: B 26 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7637 (mpp) REVERT: B 236 MET cc_start: 0.6638 (mmp) cc_final: 0.6282 (mmp) REVERT: B 288 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7589 (mp10) REVERT: B 365 MET cc_start: 0.7550 (tpp) cc_final: 0.7340 (mmt) REVERT: B 567 ASN cc_start: 0.7612 (p0) cc_final: 0.7274 (p0) REVERT: C 111 ASP cc_start: 0.8581 (t0) cc_final: 0.8327 (t0) REVERT: D 43 ARG cc_start: 0.7617 (tpm170) cc_final: 0.6854 (tpt170) REVERT: D 53 ASP cc_start: 0.7206 (m-30) cc_final: 0.6300 (t70) REVERT: F 408 GLU cc_start: 0.6716 (pt0) cc_final: 0.6490 (mt-10) REVERT: F 567 ASP cc_start: 0.8374 (t70) cc_final: 0.8160 (t0) REVERT: J 209 TRP cc_start: 0.6413 (t-100) cc_final: 0.6003 (t-100) REVERT: J 437 MET cc_start: 0.7581 (tpt) cc_final: 0.7179 (tpt) REVERT: J 567 ASP cc_start: 0.7643 (t0) cc_final: 0.7216 (t70) REVERT: E 36 ASP cc_start: 0.8418 (t0) cc_final: 0.7714 (t0) outliers start: 39 outliers final: 22 residues processed: 334 average time/residue: 0.1655 time to fit residues: 88.4409 Evaluate side-chains 321 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 297 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain J residue 186 CYS Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 465 CYS Chi-restraints excluded: chain J residue 594 LYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain K residue -20 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 106 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 218 optimal weight: 20.0000 chunk 200 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 chunk 206 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 GLN D 42 GLN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 382 HIS ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K -19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.214297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.4099 r_free = 0.4099 target = 0.167889 restraints weight = 29754.461| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.11 r_work: 0.3860 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23878 Z= 0.156 Angle : 0.547 12.633 32239 Z= 0.285 Chirality : 0.040 0.186 3618 Planarity : 0.004 0.061 4130 Dihedral : 4.229 38.949 3140 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.13 % Favored : 93.83 % Rotamer: Outliers : 1.97 % Allowed : 12.14 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2869 helix: 0.72 (0.13), residues: 1743 sheet: -1.95 (0.50), residues: 89 loop : -1.71 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 374 TYR 0.031 0.001 TYR B 510 PHE 0.028 0.001 PHE J 501 TRP 0.018 0.002 TRP B 35 HIS 0.020 0.001 HIS F 382 Details of bonding type rmsd covalent geometry : bond 0.00373 (23856) covalent geometry : angle 0.54588 (32227) hydrogen bonds : bond 0.03779 ( 1235) hydrogen bonds : angle 4.62050 ( 3648) metal coordination : bond 0.00648 ( 22) metal coordination : angle 1.96713 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7549 (ptpt) cc_final: 0.7341 (tppt) REVERT: A 297 MET cc_start: 0.7816 (ttm) cc_final: 0.7505 (tpp) REVERT: A 406 MET cc_start: 0.7176 (tpp) cc_final: 0.6567 (tpp) REVERT: A 582 MET cc_start: 0.6687 (ptm) cc_final: 0.6292 (tmm) REVERT: A 701 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7351 (tm-30) REVERT: G 65 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.6724 (mt) REVERT: I 50 MET cc_start: 0.4373 (mmt) cc_final: 0.0389 (ptm) REVERT: B 26 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7659 (mpp) REVERT: B 86 MET cc_start: 0.7649 (mmt) cc_final: 0.7350 (mmt) REVERT: B 236 MET cc_start: 0.6718 (mmp) cc_final: 0.6410 (mmp) REVERT: B 288 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: B 567 ASN cc_start: 0.7594 (p0) cc_final: 0.7294 (p0) REVERT: C 111 ASP cc_start: 0.8532 (t0) cc_final: 0.8271 (t0) REVERT: D 53 ASP cc_start: 0.7242 (m-30) cc_final: 0.6535 (t70) REVERT: F 408 GLU cc_start: 0.6716 (pt0) cc_final: 0.6504 (mt-10) REVERT: F 567 ASP cc_start: 0.8345 (t70) cc_final: 0.8085 (t0) REVERT: J 437 MET cc_start: 0.7643 (tpt) cc_final: 0.7227 (tpt) REVERT: J 472 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7753 (t80) REVERT: J 567 ASP cc_start: 0.7592 (t0) cc_final: 0.7178 (t70) REVERT: E 36 ASP cc_start: 0.8383 (t0) cc_final: 0.7719 (t0) outliers start: 51 outliers final: 30 residues processed: 339 average time/residue: 0.1623 time to fit residues: 88.3535 Evaluate side-chains 326 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 292 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain F residue 627 HIS Chi-restraints excluded: chain J residue 186 CYS Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 465 CYS Chi-restraints excluded: chain J residue 472 TYR Chi-restraints excluded: chain J residue 594 LYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain K residue -20 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.5458 > 50: distance: 14 - 143: 22.116 distance: 17 - 152: 10.985 distance: 29 - 155: 11.737 distance: 123 - 128: 5.039 distance: 128 - 129: 14.064 distance: 129 - 130: 10.833 distance: 129 - 132: 11.214 distance: 130 - 131: 27.793 distance: 130 - 133: 15.239 distance: 133 - 134: 13.859 distance: 133 - 139: 12.080 distance: 134 - 135: 13.516 distance: 134 - 137: 35.709 distance: 135 - 136: 29.538 distance: 135 - 140: 33.853 distance: 137 - 138: 30.556 distance: 138 - 139: 13.449 distance: 140 - 141: 5.509 distance: 141 - 142: 8.267 distance: 141 - 144: 6.370 distance: 142 - 143: 17.163 distance: 142 - 145: 19.516 distance: 145 - 146: 12.549 distance: 146 - 147: 12.512 distance: 146 - 149: 4.001 distance: 147 - 148: 15.882 distance: 147 - 152: 15.911 distance: 149 - 150: 32.252 distance: 149 - 151: 36.615 distance: 152 - 153: 14.511 distance: 153 - 154: 12.545 distance: 153 - 156: 9.382 distance: 154 - 155: 7.336 distance: 154 - 159: 9.143 distance: 156 - 157: 14.957 distance: 156 - 158: 6.832 distance: 159 - 160: 12.457 distance: 160 - 161: 10.030 distance: 161 - 162: 8.216 distance: 161 - 163: 16.197 distance: 163 - 164: 4.460 distance: 164 - 165: 7.330 distance: 164 - 167: 11.041 distance: 165 - 166: 11.922 distance: 165 - 171: 3.795 distance: 167 - 168: 14.997 distance: 168 - 169: 4.189 distance: 168 - 170: 15.181 distance: 171 - 172: 6.137 distance: 172 - 173: 10.510 distance: 172 - 175: 6.523 distance: 173 - 174: 14.442 distance: 173 - 176: 14.678 distance: 176 - 177: 9.330 distance: 177 - 178: 17.391 distance: 177 - 180: 20.233 distance: 178 - 179: 19.873 distance: 178 - 187: 12.258 distance: 180 - 181: 10.294 distance: 181 - 182: 11.882 distance: 181 - 183: 9.734 distance: 182 - 184: 13.692 distance: 183 - 185: 3.910 distance: 184 - 186: 26.394 distance: 187 - 188: 3.965 distance: 188 - 189: 6.618 distance: 188 - 191: 6.112 distance: 189 - 190: 13.854 distance: 189 - 198: 5.395 distance: 191 - 192: 6.374 distance: 192 - 193: 8.716 distance: 193 - 194: 5.242 distance: 195 - 196: 9.653 distance: 195 - 197: 5.807