Starting phenix.real_space_refine on Tue Jun 24 09:48:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqf_37743/06_2025/8wqf_37743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqf_37743/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqf_37743/06_2025/8wqf_37743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqf_37743/06_2025/8wqf_37743.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqf_37743/06_2025/8wqf_37743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqf_37743/06_2025/8wqf_37743.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 2.61s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ASN:plan1': 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: {'TYR:plan': 1, 'ASN:plan1': 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: {'PHE:plan': 1, 'HIS:plan': 2} 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: 15.52, per 1000 atoms: 0.66 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: 5.79 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.32 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: 8.00 Time building geometry restraints manager: 6.87 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: 8.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 59.100 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.490 ------------------------------------------------------------------------------- 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 : 8.04 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.002 TRP A 35 HIS 0.005 0.001 HIS I 48 PHE 0.049 0.002 PHE F 388 TYR 0.027 0.001 TYR J 542 ARG 0.005 0.000 ARG B 442 Details of bonding type rmsd hydrogen bonds : bond 0.13992 ( 1235) hydrogen bonds : angle 6.27184 ( 3648) metal coordination : bond 0.00818 ( 22) metal coordination : angle 2.48687 ( 12) covalent geometry : bond 0.00423 (23856) covalent geometry : angle 0.59818 (32227) *********************** 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 : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.2760 (mtp) cc_final: 0.2530 (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: 0.4403 (tp30) REVERT: A 468 GLU cc_start: 0.5940 (tm-30) cc_final: 0.5648 (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: 0.3379 (mm) REVERT: B 253 TYR cc_start: 0.0352 (m-10) cc_final: 0.0025 (m-10) REVERT: B 271 VAL cc_start: 0.0957 (p) cc_final: 0.0403 (t) REVERT: B 567 ASN cc_start: 0.7828 (p0) cc_final: 0.7140 (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: 0.7143 (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: 0.3660 time to fit residues: 247.4203 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 : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 145 optimal weight: 0.0570 chunk 115 optimal weight: 0.9990 chunk 222 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 135 optimal weight: 0.0470 chunk 165 optimal weight: 0.5980 chunk 257 optimal weight: 0.1980 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 228 GLN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.217823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.4137 r_free = 0.4137 target = 0.172159 restraints weight = 29567.329| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.25 r_work: 0.3902 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23878 Z= 0.130 Angle : 0.552 13.913 32239 Z= 0.289 Chirality : 0.039 0.187 3618 Planarity : 0.004 0.061 4130 Dihedral : 4.227 33.922 3140 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.85 % Allowed : 7.28 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2869 helix: 0.62 (0.13), residues: 1740 sheet: -2.00 (0.50), residues: 89 loop : -1.56 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 209 HIS 0.012 0.001 HIS F 476 PHE 0.034 0.001 PHE J 501 TYR 0.025 0.001 TYR J 472 ARG 0.006 0.000 ARG F 374 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 1235) hydrogen bonds : angle 4.85505 ( 3648) metal coordination : bond 0.00644 ( 22) metal coordination : angle 2.20277 ( 12) covalent geometry : bond 0.00290 (23856) covalent geometry : angle 0.55093 (32227) *********************** 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 356 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 334 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 ASP cc_start: 0.7804 (t70) cc_final: 0.7424 (t0) REVERT: A 582 MET cc_start: 0.6618 (ptm) cc_final: 0.5976 (tmm) REVERT: G 23 SER cc_start: 0.8325 (m) cc_final: 0.8103 (t) REVERT: I 50 MET cc_start: 0.4231 (mmt) cc_final: 0.0361 (ptm) REVERT: B 177 ASN cc_start: 0.7596 (t0) cc_final: 0.7350 (m-40) REVERT: B 288 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7557 (mp10) REVERT: B 567 ASN cc_start: 0.7595 (p0) cc_final: 0.7235 (t0) REVERT: C 102 GLU cc_start: 0.7754 (tp30) cc_final: 0.7465 (tp30) REVERT: C 111 ASP cc_start: 0.8505 (t0) cc_final: 0.8274 (t0) REVERT: D 43 ARG cc_start: 0.7525 (tpm170) cc_final: 0.6812 (tpt170) REVERT: D 53 ASP cc_start: 0.7141 (m-30) cc_final: 0.6281 (t70) REVERT: F 408 GLU cc_start: 0.6747 (pt0) cc_final: 0.6507 (mt-10) REVERT: F 567 ASP cc_start: 0.8233 (t70) cc_final: 0.7859 (t0) REVERT: J 437 MET cc_start: 0.7568 (tpt) cc_final: 0.7243 (tpt) REVERT: J 567 ASP cc_start: 0.7453 (t0) cc_final: 0.7040 (t70) REVERT: E 26 LYS cc_start: 0.7304 (tptt) cc_final: 0.7065 (tptt) REVERT: E 36 ASP cc_start: 0.8348 (t0) cc_final: 0.7664 (t0) outliers start: 22 outliers final: 11 residues processed: 345 average time/residue: 0.3356 time to fit residues: 184.6709 Evaluate side-chains 315 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 303 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain B residue 25 VAL 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 266 optimal weight: 0.5980 chunk 177 optimal weight: 0.3980 chunk 163 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 172 optimal weight: 0.0470 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 246 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN I 28 ASN I 48 HIS B 156 GLN ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN B 521 GLN C 51 GLN C 58 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 511 ASN F 530 ASN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 382 HIS J 489 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.216838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.170809 restraints weight = 29494.859| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.02 r_work: 0.3874 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23878 Z= 0.127 Angle : 0.530 13.668 32239 Z= 0.277 Chirality : 0.039 0.256 3618 Planarity : 0.004 0.059 4130 Dihedral : 4.142 34.002 3140 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.35 % Allowed : 9.56 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2869 helix: 0.82 (0.13), residues: 1738 sheet: -1.88 (0.51), residues: 89 loop : -1.59 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 35 HIS 0.018 0.001 HIS F 382 PHE 0.034 0.001 PHE J 501 TYR 0.031 0.001 TYR B 510 ARG 0.005 0.000 ARG F 374 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 1235) hydrogen bonds : angle 4.64674 ( 3648) metal coordination : bond 0.00585 ( 22) metal coordination : angle 1.97973 ( 12) covalent geometry : bond 0.00291 (23856) covalent geometry : angle 0.52919 (32227) *********************** 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 351 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 316 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ASP cc_start: 0.7812 (t70) cc_final: 0.7459 (t0) REVERT: A 582 MET cc_start: 0.6596 (ptm) cc_final: 0.6197 (tmm) REVERT: A 717 MET cc_start: 0.7738 (ttm) cc_final: 0.7439 (ttp) REVERT: G 23 SER cc_start: 0.8376 (m) cc_final: 0.8139 (t) REVERT: I 50 MET cc_start: 0.4137 (mmt) cc_final: 0.0343 (ptm) REVERT: B 26 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7622 (mpp) REVERT: B 86 MET cc_start: 0.7625 (mmt) cc_final: 0.7345 (mmt) REVERT: B 236 MET cc_start: 0.6700 (mmp) cc_final: 0.6297 (mmp) REVERT: B 288 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: B 365 MET cc_start: 0.7590 (tpp) cc_final: 0.7376 (mmt) REVERT: B 567 ASN cc_start: 0.7692 (p0) cc_final: 0.7410 (p0) REVERT: B 605 MET cc_start: 0.7785 (mtp) cc_final: 0.7469 (mtm) REVERT: C 111 ASP cc_start: 0.8600 (t0) cc_final: 0.8324 (t0) REVERT: D 43 ARG cc_start: 0.7550 (tpm170) cc_final: 0.6853 (tpt170) REVERT: D 53 ASP cc_start: 0.7203 (m-30) cc_final: 0.6322 (t70) REVERT: F 567 ASP cc_start: 0.8347 (t70) cc_final: 0.7975 (t0) REVERT: J 437 MET cc_start: 0.7606 (tpt) cc_final: 0.7172 (tpt) REVERT: J 567 ASP cc_start: 0.7600 (t0) cc_final: 0.7161 (t70) REVERT: E 21 ARG cc_start: 0.5820 (ttp-110) cc_final: 0.5450 (ttp-170) REVERT: E 26 LYS cc_start: 0.7323 (tptt) cc_final: 0.7113 (tptt) REVERT: E 36 ASP cc_start: 0.8462 (t0) cc_final: 0.7752 (t0) outliers start: 35 outliers final: 19 residues processed: 333 average time/residue: 0.5317 time to fit residues: 282.3374 Evaluate side-chains 314 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 293 time to evaluate : 3.027 ------------------------------------------------------------------------------- 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 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 288 GLN 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 F residue 577 LEU Chi-restraints excluded: chain J residue 186 CYS 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 K residue -20 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 222 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 198 optimal weight: 0.8980 chunk 202 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 193 GLN ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 ASN ** J 565 HIS ** 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 = 0.4501 r_free = 0.4501 target = 0.215873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.4144 r_free = 0.4144 target = 0.170490 restraints weight = 29863.878| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.02 r_work: 0.3876 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23878 Z= 0.149 Angle : 0.539 13.251 32239 Z= 0.281 Chirality : 0.040 0.180 3618 Planarity : 0.004 0.051 4130 Dihedral : 4.141 35.943 3140 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 1.62 % Allowed : 11.45 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2869 helix: 0.83 (0.13), residues: 1738 sheet: -1.88 (0.51), residues: 89 loop : -1.64 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 35 HIS 0.020 0.001 HIS F 382 PHE 0.027 0.001 PHE F 388 TYR 0.027 0.001 TYR B 510 ARG 0.006 0.000 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 1235) hydrogen bonds : angle 4.57889 ( 3648) metal coordination : bond 0.00623 ( 22) metal coordination : angle 1.92457 ( 12) covalent geometry : bond 0.00355 (23856) covalent geometry : angle 0.53737 (32227) *********************** 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 348 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7544 (ptpt) cc_final: 0.7291 (tppt) REVERT: A 413 ASP cc_start: 0.7809 (t70) cc_final: 0.7504 (t0) REVERT: A 582 MET cc_start: 0.6594 (ptm) cc_final: 0.6161 (tmm) REVERT: A 717 MET cc_start: 0.7645 (ttm) cc_final: 0.7377 (ttp) REVERT: G 23 SER cc_start: 0.8285 (m) cc_final: 0.8081 (t) REVERT: I 50 MET cc_start: 0.4127 (mmt) cc_final: 0.0267 (ptm) REVERT: B 26 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7586 (mpp) REVERT: B 86 MET cc_start: 0.7604 (mmt) cc_final: 0.7327 (mmt) REVERT: B 228 GLN cc_start: 0.7845 (mm110) cc_final: 0.7427 (pt0) REVERT: B 236 MET cc_start: 0.6715 (mmp) cc_final: 0.6411 (mmp) REVERT: B 288 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: B 365 MET cc_start: 0.7555 (tpp) cc_final: 0.7349 (mmt) REVERT: B 567 ASN cc_start: 0.7702 (p0) cc_final: 0.7372 (p0) REVERT: B 605 MET cc_start: 0.7806 (mtp) cc_final: 0.7471 (mtm) REVERT: C 111 ASP cc_start: 0.8538 (t0) cc_final: 0.8274 (t0) REVERT: D 43 ARG cc_start: 0.7635 (tpm170) cc_final: 0.6814 (tpt90) REVERT: D 53 ASP cc_start: 0.7200 (m-30) cc_final: 0.6266 (t70) REVERT: F 408 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7058 (mp0) REVERT: F 567 ASP cc_start: 0.8311 (t70) cc_final: 0.8019 (t0) REVERT: J 437 MET cc_start: 0.7581 (tpt) cc_final: 0.7276 (tpt) REVERT: J 472 TYR cc_start: 0.7976 (t80) cc_final: 0.7765 (t80) REVERT: J 473 ASN cc_start: 0.8291 (t0) cc_final: 0.7988 (t0) REVERT: J 567 ASP cc_start: 0.7602 (t0) cc_final: 0.7189 (t70) REVERT: E 26 LYS cc_start: 0.7344 (tptt) cc_final: 0.7117 (tptt) REVERT: E 36 ASP cc_start: 0.8402 (t0) cc_final: 0.7694 (t0) outliers start: 42 outliers final: 23 residues processed: 332 average time/residue: 0.3416 time to fit residues: 180.3924 Evaluate side-chains 317 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 292 time to evaluate : 2.443 ------------------------------------------------------------------------------- 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 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 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 65 ILE Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain J residue 186 CYS 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 594 LYS Chi-restraints excluded: chain K residue -20 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 60 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 255 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** F 380 ASN ** 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 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K -19 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.215696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.171881 restraints weight = 29661.772| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.89 r_work: 0.3798 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23878 Z= 0.145 Angle : 0.539 13.216 32239 Z= 0.280 Chirality : 0.039 0.248 3618 Planarity : 0.004 0.065 4130 Dihedral : 4.133 36.348 3140 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.93 % Favored : 94.04 % Rotamer: Outliers : 1.70 % Allowed : 12.49 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2869 helix: 0.84 (0.13), residues: 1735 sheet: -1.87 (0.51), residues: 89 loop : -1.66 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 209 HIS 0.027 0.001 HIS F 382 PHE 0.027 0.001 PHE F 388 TYR 0.023 0.001 TYR B 510 ARG 0.006 0.000 ARG F 374 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 1235) hydrogen bonds : angle 4.54222 ( 3648) metal coordination : bond 0.00573 ( 22) metal coordination : angle 1.86006 ( 12) covalent geometry : bond 0.00343 (23856) covalent geometry : angle 0.53776 (32227) *********************** REFINEMENT MACRO_CYCLE 5 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 342 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.7881 (mtp) cc_final: 0.7648 (mtp) REVERT: A 297 MET cc_start: 0.8188 (tpp) cc_final: 0.7911 (mpp) REVERT: A 406 MET cc_start: 0.7064 (tpp) cc_final: 0.6509 (tpp) REVERT: A 582 MET cc_start: 0.6629 (ptm) cc_final: 0.6191 (tmm) REVERT: A 688 MET cc_start: 0.6179 (mmm) cc_final: 0.5840 (mtt) REVERT: A 717 MET cc_start: 0.7610 (ttm) cc_final: 0.7355 (ttp) REVERT: G 23 SER cc_start: 0.8333 (m) cc_final: 0.8103 (t) REVERT: I 50 MET cc_start: 0.4166 (mmt) cc_final: 0.0377 (ptm) REVERT: B 26 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7652 (mpp) REVERT: B 28 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7669 (mt-10) REVERT: B 86 MET cc_start: 0.7564 (mmt) cc_final: 0.7353 (mmt) REVERT: B 236 MET cc_start: 0.6731 (mmp) cc_final: 0.6400 (mmp) REVERT: B 288 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: B 365 MET cc_start: 0.7591 (tpp) cc_final: 0.7357 (mmt) REVERT: B 410 GLU cc_start: 0.6965 (tp30) cc_final: 0.6730 (tp30) REVERT: B 567 ASN cc_start: 0.7674 (p0) cc_final: 0.7342 (p0) REVERT: B 605 MET cc_start: 0.7876 (mtp) cc_final: 0.7518 (mtm) REVERT: C 102 GLU cc_start: 0.7869 (tp30) cc_final: 0.7648 (tp30) REVERT: C 111 ASP cc_start: 0.8592 (t0) cc_final: 0.8281 (t0) REVERT: D 43 ARG cc_start: 0.7564 (tpm170) cc_final: 0.6724 (tpt90) REVERT: D 53 ASP cc_start: 0.7188 (m-30) cc_final: 0.6243 (t70) REVERT: F 408 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6995 (mp0) REVERT: F 567 ASP cc_start: 0.8448 (t70) cc_final: 0.8169 (t0) REVERT: F 587 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.8047 (mt) REVERT: J 209 TRP cc_start: 0.6498 (t-100) cc_final: 0.6232 (t-100) REVERT: J 437 MET cc_start: 0.7631 (tpt) cc_final: 0.7351 (tpt) REVERT: J 473 ASN cc_start: 0.8354 (t0) cc_final: 0.8087 (t0) REVERT: J 567 ASP cc_start: 0.7632 (t0) cc_final: 0.7207 (t70) REVERT: E 26 LYS cc_start: 0.7424 (tptt) cc_final: 0.7180 (tptt) REVERT: E 36 ASP cc_start: 0.8465 (t0) cc_final: 0.7747 (t0) REVERT: K -19 HIS cc_start: 0.6691 (m90) cc_final: 0.6394 (m90) outliers start: 44 outliers final: 28 residues processed: 325 average time/residue: 0.3424 time to fit residues: 178.1031 Evaluate side-chains 318 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 2.490 ------------------------------------------------------------------------------- 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 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 89 ARG 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 519 LEU 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 65 ILE Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 587 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 594 LYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain K residue -20 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 259 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 209 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 240 optimal weight: 0.5980 chunk 159 optimal weight: 0.0470 chunk 68 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 60 GLN ** 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 = 0.4490 r_free = 0.4490 target = 0.215694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.171443 restraints weight = 29630.297| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.85 r_work: 0.3792 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2062 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= 0.148 Angle : 0.538 13.679 32239 Z= 0.279 Chirality : 0.040 0.225 3618 Planarity : 0.004 0.050 4130 Dihedral : 4.133 37.069 3140 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.11 % Rotamer: Outliers : 1.77 % Allowed : 13.60 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2869 helix: 0.88 (0.13), residues: 1736 sheet: -1.87 (0.51), residues: 89 loop : -1.67 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 35 HIS 0.018 0.001 HIS F 382 PHE 0.028 0.001 PHE F 388 TYR 0.021 0.001 TYR B 510 ARG 0.007 0.000 ARG J 171 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 1235) hydrogen bonds : angle 4.48818 ( 3648) metal coordination : bond 0.00605 ( 22) metal coordination : angle 1.86965 ( 12) covalent geometry : bond 0.00354 (23856) covalent geometry : angle 0.53720 (32227) *********************** REFINEMENT MACRO_CYCLE 6 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 353 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 307 time to evaluate : 4.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 MET cc_start: 0.7012 (tpp) cc_final: 0.6408 (tpp) REVERT: A 582 MET cc_start: 0.6596 (ptm) cc_final: 0.6196 (tmm) REVERT: A 717 MET cc_start: 0.7538 (ttm) cc_final: 0.7295 (ttp) REVERT: G 23 SER cc_start: 0.8382 (m) cc_final: 0.8150 (t) REVERT: I 50 MET cc_start: 0.4141 (mmt) cc_final: 0.0311 (ptm) REVERT: B 26 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7677 (mpp) REVERT: B 86 MET cc_start: 0.7581 (mmt) cc_final: 0.7332 (mmt) REVERT: B 166 GLU cc_start: 0.7045 (tp30) cc_final: 0.6697 (tp30) REVERT: B 236 MET cc_start: 0.6736 (mmp) cc_final: 0.6421 (mmp) REVERT: B 253 TYR cc_start: 0.7971 (m-10) cc_final: 0.7769 (m-10) REVERT: B 288 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: B 365 MET cc_start: 0.7602 (tpp) cc_final: 0.7320 (mmt) REVERT: B 410 GLU cc_start: 0.6981 (tp30) cc_final: 0.6756 (tp30) REVERT: B 567 ASN cc_start: 0.7676 (p0) cc_final: 0.7339 (p0) REVERT: B 605 MET cc_start: 0.7848 (mtp) cc_final: 0.7456 (mtm) REVERT: C 111 ASP cc_start: 0.8626 (t0) cc_final: 0.8322 (t0) REVERT: D 41 GLU cc_start: 0.7683 (mp0) cc_final: 0.7467 (mp0) REVERT: D 43 ARG cc_start: 0.7624 (tpm170) cc_final: 0.6692 (tpt90) REVERT: D 45 TYR cc_start: 0.6590 (m-80) cc_final: 0.6285 (m-80) REVERT: D 53 ASP cc_start: 0.7217 (m-30) cc_final: 0.6264 (t70) REVERT: D 91 GLU cc_start: 0.7494 (mp0) cc_final: 0.7201 (pm20) REVERT: F 408 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6914 (mp0) REVERT: F 567 ASP cc_start: 0.8496 (t70) cc_final: 0.8238 (t0) REVERT: F 587 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8085 (mt) REVERT: J 437 MET cc_start: 0.7593 (tpt) cc_final: 0.7326 (tpp) REVERT: J 473 ASN cc_start: 0.8381 (t0) cc_final: 0.8100 (t0) REVERT: J 567 ASP cc_start: 0.7724 (t0) cc_final: 0.7341 (t70) REVERT: E 26 LYS cc_start: 0.7444 (tptt) cc_final: 0.7191 (tptt) REVERT: E 36 ASP cc_start: 0.8494 (t0) cc_final: 0.7777 (t0) outliers start: 46 outliers final: 31 residues processed: 336 average time/residue: 0.3978 time to fit residues: 214.3170 Evaluate side-chains 328 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 294 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain G residue 37 LEU 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 519 LEU Chi-restraints excluded: chain B residue 577 VAL 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 F residue 577 LEU Chi-restraints excluded: chain F residue 587 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 257 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 62 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 120 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** 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 495 ASN ** J 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.217068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.170632 restraints weight = 29791.389| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.18 r_work: 0.3878 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23878 Z= 0.116 Angle : 0.523 12.936 32239 Z= 0.271 Chirality : 0.039 0.208 3618 Planarity : 0.004 0.049 4130 Dihedral : 4.055 34.274 3140 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 1.46 % Allowed : 14.99 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2869 helix: 0.96 (0.13), residues: 1739 sheet: -1.88 (0.50), residues: 89 loop : -1.66 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 209 HIS 0.017 0.001 HIS F 382 PHE 0.027 0.001 PHE F 388 TYR 0.019 0.001 TYR C 83 ARG 0.008 0.000 ARG F 374 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 1235) hydrogen bonds : angle 4.40740 ( 3648) metal coordination : bond 0.00492 ( 22) metal coordination : angle 1.72389 ( 12) covalent geometry : bond 0.00267 (23856) covalent geometry : angle 0.52254 (32227) *********************** REFINEMENT MACRO_CYCLE 7 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 344 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 MET cc_start: 0.6894 (tpp) cc_final: 0.6293 (tpp) REVERT: A 476 MET cc_start: 0.8843 (mtp) cc_final: 0.8585 (mtp) REVERT: A 582 MET cc_start: 0.6557 (ptm) cc_final: 0.5978 (tmm) REVERT: G 23 SER cc_start: 0.8248 (m) cc_final: 0.8023 (t) REVERT: I 50 MET cc_start: 0.4006 (mmt) cc_final: 0.0247 (ptm) REVERT: B 26 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7647 (mmt) REVERT: B 28 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 166 GLU cc_start: 0.6785 (tp30) cc_final: 0.6560 (tp30) REVERT: B 236 MET cc_start: 0.6626 (mmp) cc_final: 0.6333 (mmp) REVERT: B 288 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: B 365 MET cc_start: 0.7487 (tpp) cc_final: 0.7182 (mmt) REVERT: B 410 GLU cc_start: 0.7029 (tp30) cc_final: 0.6787 (tp30) REVERT: B 567 ASN cc_start: 0.7672 (p0) cc_final: 0.7322 (p0) REVERT: B 605 MET cc_start: 0.7811 (mtp) cc_final: 0.7431 (mtm) REVERT: B 730 TYR cc_start: 0.7402 (m-10) cc_final: 0.7183 (m-10) REVERT: C 111 ASP cc_start: 0.8597 (t0) cc_final: 0.8282 (t0) REVERT: D 45 TYR cc_start: 0.6522 (m-80) cc_final: 0.6182 (m-80) REVERT: D 53 ASP cc_start: 0.7168 (m-30) cc_final: 0.6459 (t70) REVERT: D 91 GLU cc_start: 0.7474 (mp0) cc_final: 0.7215 (pm20) REVERT: F 408 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6854 (mp0) REVERT: F 567 ASP cc_start: 0.8425 (t70) cc_final: 0.8094 (t0) REVERT: F 587 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8046 (mt) REVERT: F 615 GLN cc_start: 0.7994 (mp10) cc_final: 0.7770 (mp10) REVERT: J 159 MET cc_start: 0.4996 (mtt) cc_final: 0.4727 (mtt) REVERT: J 426 LYS cc_start: 0.8638 (mppt) cc_final: 0.8411 (mmtm) REVERT: J 437 MET cc_start: 0.7479 (tpt) cc_final: 0.7276 (tpp) REVERT: J 473 ASN cc_start: 0.8350 (t0) cc_final: 0.8052 (t0) REVERT: J 567 ASP cc_start: 0.7594 (t0) cc_final: 0.7175 (t70) REVERT: E 26 LYS cc_start: 0.7363 (tptt) cc_final: 0.7096 (tptt) REVERT: E 36 ASP cc_start: 0.8475 (t0) cc_final: 0.7777 (t0) outliers start: 38 outliers final: 30 residues processed: 330 average time/residue: 0.3828 time to fit residues: 203.1628 Evaluate side-chains 330 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 297 time to evaluate : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain G residue 37 LEU 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 56 CYS 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 398 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 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 577 LEU Chi-restraints excluded: chain F residue 587 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 594 LYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain K residue -20 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 170 optimal weight: 0.9980 chunk 273 optimal weight: 0.6980 chunk 183 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 263 optimal weight: 0.9980 chunk 255 optimal weight: 0.5980 chunk 242 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** 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 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.215513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.167364 restraints weight = 29687.839| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.24 r_work: 0.3824 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23878 Z= 0.144 Angle : 0.538 12.398 32239 Z= 0.280 Chirality : 0.040 0.199 3618 Planarity : 0.004 0.049 4130 Dihedral : 4.085 35.683 3140 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.21 % Rotamer: Outliers : 1.66 % Allowed : 15.26 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2869 helix: 0.92 (0.13), residues: 1742 sheet: -1.68 (0.52), residues: 83 loop : -1.68 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 72 HIS 0.017 0.001 HIS F 382 PHE 0.027 0.001 PHE F 388 TYR 0.020 0.001 TYR C 83 ARG 0.007 0.000 ARG F 374 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 1235) hydrogen bonds : angle 4.40958 ( 3648) metal coordination : bond 0.00591 ( 22) metal coordination : angle 1.93086 ( 12) covalent geometry : bond 0.00344 (23856) covalent geometry : angle 0.53684 (32227) *********************** REFINEMENT MACRO_CYCLE 8 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 345 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 302 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7349 (ptp-110) REVERT: A 297 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7915 (mpp) REVERT: A 406 MET cc_start: 0.6875 (tpp) cc_final: 0.6282 (tpp) REVERT: A 582 MET cc_start: 0.6627 (ptm) cc_final: 0.6083 (tmm) REVERT: G 23 SER cc_start: 0.8278 (m) cc_final: 0.8032 (t) REVERT: I 50 MET cc_start: 0.4015 (mmt) cc_final: 0.0211 (ptm) REVERT: B 26 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7665 (mpp) REVERT: B 28 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7783 (mt-10) REVERT: B 166 GLU cc_start: 0.6930 (tp30) cc_final: 0.6640 (tp30) REVERT: B 236 MET cc_start: 0.6706 (mmp) cc_final: 0.6408 (mmp) REVERT: B 288 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7444 (mp10) REVERT: B 365 MET cc_start: 0.7516 (tpp) cc_final: 0.7207 (mmt) REVERT: B 410 GLU cc_start: 0.7068 (tp30) cc_final: 0.6802 (tp30) REVERT: B 567 ASN cc_start: 0.7676 (p0) cc_final: 0.7298 (p0) REVERT: B 605 MET cc_start: 0.7862 (mtp) cc_final: 0.7454 (mtm) REVERT: B 730 TYR cc_start: 0.7435 (m-10) cc_final: 0.7224 (m-10) REVERT: C 111 ASP cc_start: 0.8667 (t0) cc_final: 0.8343 (t0) REVERT: D 43 ARG cc_start: 0.7631 (tpm170) cc_final: 0.7174 (tpm170) REVERT: D 45 TYR cc_start: 0.6491 (m-80) cc_final: 0.6144 (m-80) REVERT: D 53 ASP cc_start: 0.7167 (m-30) cc_final: 0.6409 (t70) REVERT: D 91 GLU cc_start: 0.7506 (mp0) cc_final: 0.7231 (pm20) REVERT: F 408 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6868 (mp0) REVERT: F 587 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8055 (mt) REVERT: J 159 MET cc_start: 0.5071 (mtt) cc_final: 0.4790 (mtt) REVERT: J 209 TRP cc_start: 0.6741 (t-100) cc_final: 0.6139 (t-100) REVERT: J 426 LYS cc_start: 0.8664 (mppt) cc_final: 0.8437 (mmtm) REVERT: J 437 MET cc_start: 0.7576 (tpt) cc_final: 0.7268 (tpp) REVERT: J 473 ASN cc_start: 0.8396 (t0) cc_final: 0.8097 (t0) REVERT: J 482 ARG cc_start: 0.8029 (ptp-110) cc_final: 0.7753 (ptp-110) REVERT: J 567 ASP cc_start: 0.7753 (t0) cc_final: 0.7380 (t70) REVERT: E 26 LYS cc_start: 0.7380 (tptt) cc_final: 0.7060 (tptt) REVERT: E 36 ASP cc_start: 0.8543 (t0) cc_final: 0.7825 (t0) outliers start: 43 outliers final: 32 residues processed: 331 average time/residue: 0.4050 time to fit residues: 214.1584 Evaluate side-chains 333 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 3.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain G residue 37 LEU 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 56 CYS Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain B residue 20 THR 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 398 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 577 VAL 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 65 ILE Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 587 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 227 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 chunk 213 optimal weight: 30.0000 chunk 222 optimal weight: 8.9990 chunk 271 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 377 ASN ** 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 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.212606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.166008 restraints weight = 29460.428| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.20 r_work: 0.3826 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23878 Z= 0.142 Angle : 0.547 12.900 32239 Z= 0.285 Chirality : 0.039 0.212 3618 Planarity : 0.004 0.049 4130 Dihedral : 4.089 35.071 3140 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.28 % Rotamer: Outliers : 1.66 % Allowed : 15.68 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2869 helix: 0.94 (0.13), residues: 1744 sheet: -1.80 (0.54), residues: 79 loop : -1.69 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 72 HIS 0.019 0.001 HIS F 382 PHE 0.025 0.001 PHE F 388 TYR 0.020 0.001 TYR C 83 ARG 0.007 0.000 ARG J 171 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 1235) hydrogen bonds : angle 4.38738 ( 3648) metal coordination : bond 0.00566 ( 22) metal coordination : angle 1.84308 ( 12) covalent geometry : bond 0.00338 (23856) covalent geometry : angle 0.54606 (32227) *********************** REFINEMENT MACRO_CYCLE 9 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 341 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 298 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7332 (ptp-110) REVERT: A 406 MET cc_start: 0.6940 (tpp) cc_final: 0.6340 (tpp) REVERT: A 582 MET cc_start: 0.6573 (ptm) cc_final: 0.6088 (tmm) REVERT: G 23 SER cc_start: 0.8263 (m) cc_final: 0.8032 (t) REVERT: I 50 MET cc_start: 0.4015 (mmt) cc_final: 0.0178 (ptm) REVERT: B 26 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7739 (mpp) REVERT: B 28 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7793 (mt-10) REVERT: B 166 GLU cc_start: 0.6884 (tp30) cc_final: 0.6534 (tp30) REVERT: B 229 GLU cc_start: 0.6288 (pt0) cc_final: 0.6037 (pt0) REVERT: B 236 MET cc_start: 0.6796 (mmp) cc_final: 0.6455 (mmp) REVERT: B 288 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: B 365 MET cc_start: 0.7524 (tpp) cc_final: 0.7218 (mmt) REVERT: B 406 MET cc_start: 0.7573 (mmt) cc_final: 0.7281 (mmm) REVERT: B 410 GLU cc_start: 0.7088 (tp30) cc_final: 0.6881 (tp30) REVERT: B 567 ASN cc_start: 0.7686 (p0) cc_final: 0.7329 (p0) REVERT: B 605 MET cc_start: 0.7837 (mtp) cc_final: 0.7436 (mtm) REVERT: B 730 TYR cc_start: 0.7437 (m-10) cc_final: 0.7225 (m-10) REVERT: C 111 ASP cc_start: 0.8676 (t0) cc_final: 0.8362 (t0) REVERT: D 45 TYR cc_start: 0.6575 (m-80) cc_final: 0.6276 (m-80) REVERT: D 53 ASP cc_start: 0.7218 (m-30) cc_final: 0.6572 (t70) REVERT: D 91 GLU cc_start: 0.7481 (mp0) cc_final: 0.7215 (pm20) REVERT: F 399 ASN cc_start: 0.8352 (m-40) cc_final: 0.7772 (t0) REVERT: F 408 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6887 (mp0) REVERT: F 587 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8071 (mt) REVERT: F 615 GLN cc_start: 0.8063 (mp10) cc_final: 0.7806 (mp10) REVERT: J 209 TRP cc_start: 0.6799 (t-100) cc_final: 0.6124 (t-100) REVERT: J 241 HIS cc_start: 0.7078 (t-90) cc_final: 0.6640 (t-90) REVERT: J 308 CYS cc_start: 0.7473 (m) cc_final: 0.6902 (p) REVERT: J 437 MET cc_start: 0.7586 (tpt) cc_final: 0.7278 (tpp) REVERT: J 473 ASN cc_start: 0.8347 (t0) cc_final: 0.8058 (t0) REVERT: J 482 ARG cc_start: 0.8090 (ptp-110) cc_final: 0.7812 (ptp-110) REVERT: J 567 ASP cc_start: 0.7696 (t0) cc_final: 0.7332 (t70) REVERT: E 26 LYS cc_start: 0.7401 (tptt) cc_final: 0.7093 (tptt) REVERT: E 36 ASP cc_start: 0.8523 (t0) cc_final: 0.7825 (t0) outliers start: 43 outliers final: 35 residues processed: 325 average time/residue: 0.3941 time to fit residues: 206.1341 Evaluate side-chains 334 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 295 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain G residue 37 LEU 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 56 CYS Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 89 LYS Chi-restraints excluded: chain B residue 20 THR 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 398 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 577 VAL 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 65 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 587 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 133 optimal weight: 0.0170 chunk 148 optimal weight: 0.3980 chunk 183 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 248 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 224 optimal weight: 20.0000 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 377 ASN ** 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 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.212725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.166956 restraints weight = 29709.115| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.16 r_work: 0.3848 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23878 Z= 0.140 Angle : 0.544 12.749 32239 Z= 0.284 Chirality : 0.039 0.209 3618 Planarity : 0.004 0.049 4130 Dihedral : 4.090 35.239 3140 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.54 % Allowed : 15.72 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.16), residues: 2869 helix: 0.95 (0.13), residues: 1744 sheet: -1.84 (0.54), residues: 79 loop : -1.68 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP I 72 HIS 0.018 0.001 HIS F 382 PHE 0.028 0.001 PHE A 651 TYR 0.021 0.001 TYR C 83 ARG 0.008 0.000 ARG J 171 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 1235) hydrogen bonds : angle 4.37448 ( 3648) metal coordination : bond 0.00578 ( 22) metal coordination : angle 1.80533 ( 12) covalent geometry : bond 0.00334 (23856) covalent geometry : angle 0.54319 (32227) ********************** REFINEMENT MACRO_CYCLE 10 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 341 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7280 (ptp-110) REVERT: A 406 MET cc_start: 0.7157 (tpp) cc_final: 0.6555 (tpp) REVERT: A 582 MET cc_start: 0.6889 (ptm) cc_final: 0.6455 (tmm) REVERT: G 23 SER cc_start: 0.8251 (m) cc_final: 0.8042 (t) REVERT: I 50 MET cc_start: 0.4330 (mmt) cc_final: 0.0478 (ptm) REVERT: B 26 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7783 (mpp) REVERT: B 28 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7648 (mt-10) REVERT: B 166 GLU cc_start: 0.6899 (tp30) cc_final: 0.6669 (tp30) REVERT: B 229 GLU cc_start: 0.6261 (pt0) cc_final: 0.5969 (pt0) REVERT: B 236 MET cc_start: 0.6864 (mmp) cc_final: 0.6556 (mmp) REVERT: B 288 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: B 365 MET cc_start: 0.7528 (tpp) cc_final: 0.7245 (mmt) REVERT: B 406 MET cc_start: 0.7609 (mmt) cc_final: 0.7358 (mmm) REVERT: B 567 ASN cc_start: 0.7670 (p0) cc_final: 0.7340 (p0) REVERT: B 730 TYR cc_start: 0.7490 (m-10) cc_final: 0.7283 (m-10) REVERT: C 111 ASP cc_start: 0.8569 (t0) cc_final: 0.8287 (t0) REVERT: D 45 TYR cc_start: 0.6687 (m-80) cc_final: 0.6405 (m-80) REVERT: D 53 ASP cc_start: 0.7236 (m-30) cc_final: 0.6782 (t70) REVERT: F 399 ASN cc_start: 0.8304 (m-40) cc_final: 0.7836 (t0) REVERT: F 408 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6917 (mp0) REVERT: F 587 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8096 (mt) REVERT: J 209 TRP cc_start: 0.6673 (t-100) cc_final: 0.6049 (t-100) REVERT: J 241 HIS cc_start: 0.6929 (t-90) cc_final: 0.6664 (t-90) REVERT: J 308 CYS cc_start: 0.7550 (m) cc_final: 0.7066 (p) REVERT: J 473 ASN cc_start: 0.8250 (t0) cc_final: 0.8002 (t0) REVERT: J 567 ASP cc_start: 0.7580 (t0) cc_final: 0.7270 (t70) REVERT: E 36 ASP cc_start: 0.8360 (t0) cc_final: 0.7742 (t0) outliers start: 40 outliers final: 35 residues processed: 325 average time/residue: 0.3306 time to fit residues: 173.7385 Evaluate side-chains 336 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain G residue 37 LEU 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 56 CYS Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 89 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 177 ASN 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 398 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 577 VAL 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 65 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 587 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 271 optimal weight: 0.9990 chunk 273 optimal weight: 0.5980 chunk 253 optimal weight: 0.9980 chunk 222 optimal weight: 10.0000 chunk 258 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 198 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 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 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.207071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.166791 restraints weight = 28943.767| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.64 r_work: 0.3751 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23878 Z= 0.152 Angle : 0.560 12.754 32239 Z= 0.291 Chirality : 0.040 0.190 3618 Planarity : 0.004 0.049 4130 Dihedral : 4.137 36.339 3140 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.50 % Allowed : 16.07 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2869 helix: 0.94 (0.13), residues: 1740 sheet: -1.88 (0.53), residues: 79 loop : -1.70 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 72 HIS 0.017 0.001 HIS F 382 PHE 0.026 0.001 PHE A 651 TYR 0.023 0.001 TYR J 163 ARG 0.008 0.000 ARG J 171 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 1235) hydrogen bonds : angle 4.39217 ( 3648) metal coordination : bond 0.00621 ( 22) metal coordination : angle 1.87558 ( 12) covalent geometry : bond 0.00367 (23856) covalent geometry : angle 0.55922 (32227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17022.93 seconds wall clock time: 302 minutes 28.91 seconds (18148.91 seconds total)