Starting phenix.real_space_refine on Wed May 15 05:14:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqf_37743/05_2024/8wqf_37743.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqf_37743/05_2024/8wqf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqf_37743/05_2024/8wqf_37743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqf_37743/05_2024/8wqf_37743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqf_37743/05_2024/8wqf_37743.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqf_37743/05_2024/8wqf_37743.pdb" } 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 Residue "A TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 339": "OD1" <-> "OD2" Residue "J TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 11.58, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 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: 9.46 Conformation dependent library (CDL) restraints added in 5.0 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: 2.14 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: 7.93 Time building geometry restraints manager: 10.06 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: 99.53 - 106.45: 560 106.45 - 113.36: 13201 113.36 - 120.28: 8730 120.28 - 127.19: 9503 127.19 - 134.11: 233 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 2.440 nonbonded pdb=" OG SER J 393 " pdb=" O HIS J 502 " model vdw 2.219 2.440 nonbonded pdb=" OG SER F 393 " pdb=" O HIS F 502 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR J 302 " pdb=" OE1 GLU J 333 " model vdw 2.226 2.440 nonbonded pdb=" OH TYR J 449 " pdb=" O PRO J 497 " model vdw 2.226 2.440 ... (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 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: 9.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.030 Extract box with map and model: 28.800 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 64.160 Find NCS groups from input model: 1.320 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.430 ------------------------------------------------------------------------------- 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 23856 Z= 0.274 Angle : 0.598 13.100 32227 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 2.819 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: 0.3779 time to fit residues: 255.4305 Evaluate side-chains 302 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.678 ------------------------------------------------------------------------------- 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: 0.0870 chunk 119 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 145 optimal weight: 0.1980 chunk 115 optimal weight: 0.6980 chunk 222 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 257 optimal weight: 0.1980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 92 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5481 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23856 Z= 0.176 Angle : 0.534 13.544 32227 Z= 0.280 Chirality : 0.039 0.188 3618 Planarity : 0.004 0.061 4130 Dihedral : 4.213 33.362 3140 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.04 % Allowed : 7.40 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.16), residues: 2869 helix: 0.65 (0.13), residues: 1738 sheet: -1.46 (0.58), residues: 64 loop : -1.55 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 209 HIS 0.010 0.001 HIS F 476 PHE 0.036 0.001 PHE J 501 TYR 0.024 0.001 TYR J 472 ARG 0.006 0.000 ARG F 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 331 time to evaluate : 2.568 Fit side-chains revert: symmetry clash REVERT: G 70 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7056 (mt) REVERT: I 50 MET cc_start: 0.4727 (mmt) cc_final: 0.1900 (ptm) REVERT: B 86 MET cc_start: 0.7891 (mmt) cc_final: 0.7538 (mmt) REVERT: B 567 ASN cc_start: 0.7700 (p0) cc_final: 0.7209 (t0) REVERT: C 102 GLU cc_start: 0.7554 (tp30) cc_final: 0.7324 (tp30) REVERT: D 43 ARG cc_start: 0.7333 (tpm170) cc_final: 0.7045 (tpt90) REVERT: D 53 ASP cc_start: 0.7390 (m-30) cc_final: 0.6614 (t70) REVERT: F 408 GLU cc_start: 0.6460 (pt0) cc_final: 0.6167 (mt-10) REVERT: F 530 ASN cc_start: 0.7429 (m-40) cc_final: 0.7095 (m-40) REVERT: F 567 ASP cc_start: 0.8413 (t70) cc_final: 0.8111 (t0) REVERT: F 615 GLN cc_start: 0.7852 (mp10) cc_final: 0.7594 (mp10) REVERT: J 567 ASP cc_start: 0.7588 (t0) cc_final: 0.7088 (t70) outliers start: 27 outliers final: 15 residues processed: 344 average time/residue: 0.3757 time to fit residues: 207.0354 Evaluate side-chains 311 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 295 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 70 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 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 341 ILE Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 465 CYS Chi-restraints excluded: chain E residue 51 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 214 optimal weight: 20.0000 chunk 175 optimal weight: 0.4980 chunk 71 optimal weight: 5.9990 chunk 258 optimal weight: 0.0010 chunk 279 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 chunk 256 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 228 GLN A 234 GLN A 463 GLN I 28 ASN I 48 HIS B 156 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 511 ASN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 382 HIS ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN E 92 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5544 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23856 Z= 0.285 Angle : 0.563 12.684 32227 Z= 0.294 Chirality : 0.041 0.249 3618 Planarity : 0.004 0.057 4130 Dihedral : 4.258 37.522 3140 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.70 % Allowed : 10.75 % Favored : 87.55 % 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: -0.39 (0.16), residues: 2869 helix: 0.65 (0.13), residues: 1735 sheet: -1.86 (0.55), residues: 70 loop : -1.63 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 209 HIS 0.010 0.001 HIS F 382 PHE 0.036 0.002 PHE J 501 TYR 0.036 0.002 TYR B 510 ARG 0.005 0.000 ARG F 374 *********************** 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 362 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 318 time to evaluate : 2.829 Fit side-chains revert: symmetry clash REVERT: I 50 MET cc_start: 0.4980 (mmt) cc_final: 0.1970 (ptm) REVERT: B 26 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7550 (mpp) REVERT: B 86 MET cc_start: 0.7934 (mmt) cc_final: 0.7580 (mmt) REVERT: B 567 ASN cc_start: 0.7731 (p0) cc_final: 0.7168 (t0) REVERT: D 43 ARG cc_start: 0.7381 (tpm170) cc_final: 0.7170 (tpt90) REVERT: D 53 ASP cc_start: 0.7388 (m-30) cc_final: 0.6698 (t70) REVERT: F 408 GLU cc_start: 0.6491 (pt0) cc_final: 0.6262 (mt-10) REVERT: F 530 ASN cc_start: 0.7486 (m-40) cc_final: 0.7107 (m-40) REVERT: F 567 ASP cc_start: 0.8659 (t70) cc_final: 0.8444 (t0) REVERT: F 615 GLN cc_start: 0.7866 (mp10) cc_final: 0.7495 (mp10) REVERT: J 530 ASN cc_start: 0.8312 (m110) cc_final: 0.8083 (m-40) REVERT: J 567 ASP cc_start: 0.7946 (t0) cc_final: 0.7598 (t0) outliers start: 44 outliers final: 30 residues processed: 342 average time/residue: 0.3501 time to fit residues: 189.0437 Evaluate side-chains 331 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 300 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain G residue 37 LEU 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 61 THR Chi-restraints excluded: chain B residue 89 ARG 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 294 MET Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain F residue 511 ASN Chi-restraints excluded: chain F residue 577 LEU 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 E residue 51 ASP 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 255 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 173 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 274 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 245 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B 508 GLN D 42 GLN ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 511 ASN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5539 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23856 Z= 0.245 Angle : 0.542 13.098 32227 Z= 0.281 Chirality : 0.039 0.190 3618 Planarity : 0.004 0.051 4130 Dihedral : 4.227 37.098 3140 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.12 % Allowed : 12.72 % Favored : 85.16 % 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: -0.28 (0.16), residues: 2869 helix: 0.76 (0.13), residues: 1731 sheet: -1.59 (0.56), residues: 73 loop : -1.64 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP J 209 HIS 0.020 0.001 HIS F 382 PHE 0.024 0.001 PHE F 388 TYR 0.021 0.001 TYR B 510 ARG 0.005 0.000 ARG F 374 *********************** 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 352 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 297 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 50 MET cc_start: 0.4795 (mmt) cc_final: 0.1959 (ptm) REVERT: B 26 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7509 (mpp) REVERT: B 86 MET cc_start: 0.7923 (mmt) cc_final: 0.7590 (mmt) REVERT: B 567 ASN cc_start: 0.7737 (p0) cc_final: 0.7136 (t0) REVERT: D 43 ARG cc_start: 0.7459 (tpm170) cc_final: 0.7099 (tpt90) REVERT: D 53 ASP cc_start: 0.7424 (m-30) cc_final: 0.6678 (t70) REVERT: F 408 GLU cc_start: 0.6509 (pt0) cc_final: 0.6258 (mt-10) REVERT: F 530 ASN cc_start: 0.7444 (m-40) cc_final: 0.7068 (m-40) REVERT: F 567 ASP cc_start: 0.8598 (t70) cc_final: 0.8323 (t0) REVERT: J 530 ASN cc_start: 0.8313 (m110) cc_final: 0.8088 (m-40) REVERT: J 567 ASP cc_start: 0.7875 (t0) cc_final: 0.7536 (t0) outliers start: 55 outliers final: 35 residues processed: 333 average time/residue: 0.3402 time to fit residues: 180.3036 Evaluate side-chains 324 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 288 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP 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 452 ASP 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 83 VAL Chi-restraints excluded: chain B residue 89 ARG 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 294 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 577 LEU Chi-restraints excluded: chain F residue 627 HIS 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 E residue 38 VAL Chi-restraints excluded: chain E residue 51 ASP 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 228 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 246 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K -19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5548 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23856 Z= 0.263 Angle : 0.551 13.646 32227 Z= 0.286 Chirality : 0.040 0.254 3618 Planarity : 0.004 0.065 4130 Dihedral : 4.243 37.629 3140 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.08 % Allowed : 14.03 % Favored : 83.89 % 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: -0.32 (0.16), residues: 2869 helix: 0.72 (0.13), residues: 1733 sheet: -1.57 (0.57), residues: 73 loop : -1.64 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 209 HIS 0.015 0.001 HIS K -19 PHE 0.025 0.001 PHE F 388 TYR 0.032 0.001 TYR B 510 ARG 0.006 0.000 ARG F 374 *********************** 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 359 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 305 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 50 MET cc_start: 0.4887 (mmt) cc_final: 0.2025 (ptm) REVERT: B 26 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7615 (mpp) REVERT: B 86 MET cc_start: 0.7930 (mmt) cc_final: 0.7603 (mmt) REVERT: B 567 ASN cc_start: 0.7719 (p0) cc_final: 0.7123 (t0) REVERT: B 678 MET cc_start: 0.7241 (mmm) cc_final: 0.6839 (tpt) REVERT: D 43 ARG cc_start: 0.7459 (tpm170) cc_final: 0.7082 (tpt90) REVERT: D 53 ASP cc_start: 0.7460 (m-30) cc_final: 0.6707 (t70) REVERT: F 382 HIS cc_start: 0.7680 (p-80) cc_final: 0.7293 (p-80) REVERT: F 408 GLU cc_start: 0.6518 (pt0) cc_final: 0.6234 (mt-10) REVERT: F 530 ASN cc_start: 0.7424 (m-40) cc_final: 0.7041 (m-40) REVERT: F 567 ASP cc_start: 0.8646 (t70) cc_final: 0.8372 (t0) REVERT: J 530 ASN cc_start: 0.8332 (m110) cc_final: 0.8120 (m-40) REVERT: J 567 ASP cc_start: 0.7922 (t0) cc_final: 0.7574 (t0) outliers start: 54 outliers final: 41 residues processed: 339 average time/residue: 0.3537 time to fit residues: 190.0454 Evaluate side-chains 337 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 295 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 THR 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 452 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 89 ARG 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 294 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 THR 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 653 ILE Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 577 LEU 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 E residue 51 ASP 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 92 optimal weight: 0.8980 chunk 247 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 274 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23856 Z= 0.240 Angle : 0.546 13.509 32227 Z= 0.282 Chirality : 0.040 0.225 3618 Planarity : 0.004 0.050 4130 Dihedral : 4.224 37.289 3140 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.97 % Allowed : 15.72 % Favored : 82.31 % 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: -0.28 (0.16), residues: 2869 helix: 0.76 (0.13), residues: 1736 sheet: -1.49 (0.60), residues: 64 loop : -1.68 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 209 HIS 0.011 0.001 HIS F 382 PHE 0.026 0.001 PHE F 388 TYR 0.029 0.001 TYR B 510 ARG 0.006 0.000 ARG F 374 *********************** 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 fitting. rotamer outliers: 51 poor density : 302 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 50 MET cc_start: 0.4851 (mmt) cc_final: 0.1987 (ptm) REVERT: B 26 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7658 (mpp) REVERT: B 86 MET cc_start: 0.7939 (mmt) cc_final: 0.7577 (mmt) REVERT: B 567 ASN cc_start: 0.7695 (p0) cc_final: 0.7324 (p0) REVERT: D 43 ARG cc_start: 0.7450 (tpm170) cc_final: 0.7052 (tpt90) REVERT: D 53 ASP cc_start: 0.7442 (m-30) cc_final: 0.6714 (t70) REVERT: F 382 HIS cc_start: 0.7773 (p-80) cc_final: 0.7329 (p-80) REVERT: F 408 GLU cc_start: 0.6546 (pt0) cc_final: 0.6277 (mt-10) REVERT: F 530 ASN cc_start: 0.7416 (m-40) cc_final: 0.7029 (m-40) REVERT: J 426 LYS cc_start: 0.8685 (mppt) cc_final: 0.8479 (mmtm) REVERT: J 567 ASP cc_start: 0.7890 (t0) cc_final: 0.7545 (t0) outliers start: 51 outliers final: 43 residues processed: 335 average time/residue: 0.3641 time to fit residues: 194.3238 Evaluate side-chains 332 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 288 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP 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 249 ARG Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain B residue 20 THR 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 177 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 577 LEU 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 E residue 49 ILE Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain K residue -20 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 156 optimal weight: 0.6980 chunk 200 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 153 optimal weight: 0.7980 chunk 273 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** F 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5527 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23856 Z= 0.202 Angle : 0.533 12.570 32227 Z= 0.277 Chirality : 0.039 0.205 3618 Planarity : 0.004 0.068 4130 Dihedral : 4.188 35.624 3140 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.08 % Allowed : 16.07 % Favored : 81.85 % 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: -0.18 (0.16), residues: 2869 helix: 0.85 (0.13), residues: 1736 sheet: -1.43 (0.60), residues: 64 loop : -1.65 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 209 HIS 0.009 0.001 HIS F 382 PHE 0.025 0.001 PHE F 388 TYR 0.024 0.001 TYR C 83 ARG 0.007 0.000 ARG J 171 *********************** 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 353 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 299 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 50 MET cc_start: 0.4770 (mmt) cc_final: 0.1958 (ptm) REVERT: B 26 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7671 (mpp) REVERT: B 86 MET cc_start: 0.7913 (mmt) cc_final: 0.7540 (mmt) REVERT: B 567 ASN cc_start: 0.7676 (p0) cc_final: 0.7310 (p0) REVERT: D 43 ARG cc_start: 0.7436 (tpm170) cc_final: 0.6982 (tpt90) REVERT: D 53 ASP cc_start: 0.7424 (m-30) cc_final: 0.6715 (t70) REVERT: D 70 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8291 (mp10) REVERT: F 382 HIS cc_start: 0.7757 (p-80) cc_final: 0.7337 (p-80) REVERT: F 408 GLU cc_start: 0.6531 (pt0) cc_final: 0.6278 (mt-10) REVERT: F 422 MET cc_start: 0.7837 (ttm) cc_final: 0.7621 (mtm) REVERT: F 530 ASN cc_start: 0.7386 (m-40) cc_final: 0.7002 (m-40) REVERT: J 426 LYS cc_start: 0.8660 (mppt) cc_final: 0.8431 (mmtm) REVERT: J 567 ASP cc_start: 0.7885 (t0) cc_final: 0.7543 (t0) outliers start: 54 outliers final: 42 residues processed: 338 average time/residue: 0.3698 time to fit residues: 202.2722 Evaluate side-chains 338 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 294 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain B residue 20 THR 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 177 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 505 ILE 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 712 ASN Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 577 LEU 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 E residue 38 VAL Chi-restraints excluded: chain E residue 51 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 0.0370 chunk 109 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 186 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 249 optimal weight: 1.9990 overall best weight: 0.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 108 ASN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5541 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23856 Z= 0.238 Angle : 0.546 13.606 32227 Z= 0.285 Chirality : 0.040 0.197 3618 Planarity : 0.004 0.072 4130 Dihedral : 4.192 36.020 3140 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.31 % Allowed : 16.30 % Favored : 81.39 % 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: 0.84 (0.13), residues: 1737 sheet: -1.44 (0.60), residues: 64 loop : -1.68 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 209 HIS 0.008 0.001 HIS F 382 PHE 0.029 0.001 PHE F 388 TYR 0.025 0.001 TYR C 83 ARG 0.007 0.000 ARG J 171 *********************** 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 360 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 300 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 50 MET cc_start: 0.4843 (mmt) cc_final: 0.1997 (ptm) REVERT: B 26 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7687 (mpp) REVERT: B 86 MET cc_start: 0.7933 (mmt) cc_final: 0.7598 (mmt) REVERT: B 567 ASN cc_start: 0.7675 (p0) cc_final: 0.7308 (p0) REVERT: D 53 ASP cc_start: 0.7448 (m-30) cc_final: 0.6932 (t70) REVERT: D 70 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8294 (mp10) REVERT: F 382 HIS cc_start: 0.7816 (p-80) cc_final: 0.7457 (p-80) REVERT: F 399 ASN cc_start: 0.8329 (m-40) cc_final: 0.7790 (t0) REVERT: F 408 GLU cc_start: 0.6533 (pt0) cc_final: 0.6283 (mt-10) REVERT: F 422 MET cc_start: 0.7844 (ttm) cc_final: 0.7626 (mtm) REVERT: F 530 ASN cc_start: 0.7322 (m-40) cc_final: 0.6946 (m-40) REVERT: J 567 ASP cc_start: 0.7894 (t0) cc_final: 0.7544 (t0) outliers start: 60 outliers final: 48 residues processed: 341 average time/residue: 0.3403 time to fit residues: 186.4079 Evaluate side-chains 341 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 291 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 89 ARG 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 294 MET Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 480 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 712 ASN Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain F residue 363 CYS Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 577 LEU 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 E residue 49 ILE Chi-restraints excluded: chain E residue 51 ASP 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 262 optimal weight: 0.3980 chunk 239 optimal weight: 0.4980 chunk 255 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 254 optimal weight: 0.5980 chunk 167 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 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 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23856 Z= 0.207 Angle : 0.542 13.062 32227 Z= 0.282 Chirality : 0.039 0.239 3618 Planarity : 0.004 0.074 4130 Dihedral : 4.161 34.491 3140 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.81 % Allowed : 16.92 % Favored : 81.27 % 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: 0.91 (0.13), residues: 1737 sheet: -1.47 (0.58), residues: 73 loop : -1.64 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 209 HIS 0.007 0.001 HIS F 382 PHE 0.028 0.001 PHE A 651 TYR 0.026 0.001 TYR C 83 ARG 0.008 0.000 ARG J 171 *********************** 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 345 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 298 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 50 MET cc_start: 0.4876 (mmt) cc_final: 0.1990 (ptm) REVERT: B 26 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7752 (mpp) REVERT: B 86 MET cc_start: 0.7884 (mmt) cc_final: 0.7445 (mmt) REVERT: B 567 ASN cc_start: 0.7655 (p0) cc_final: 0.7279 (p0) REVERT: D 53 ASP cc_start: 0.7472 (m-30) cc_final: 0.6951 (t70) REVERT: D 70 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8302 (mp10) REVERT: F 399 ASN cc_start: 0.8336 (m-40) cc_final: 0.7792 (t0) REVERT: F 408 GLU cc_start: 0.6526 (pt0) cc_final: 0.6112 (mt-10) REVERT: F 422 MET cc_start: 0.7849 (ttm) cc_final: 0.7646 (mtm) REVERT: F 530 ASN cc_start: 0.7355 (m-40) cc_final: 0.6946 (m-40) REVERT: J 567 ASP cc_start: 0.7883 (t0) cc_final: 0.7542 (t0) outliers start: 47 outliers final: 43 residues processed: 329 average time/residue: 0.3418 time to fit residues: 180.0040 Evaluate side-chains 338 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 293 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain B residue 20 THR 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 177 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 505 ILE 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 712 ASN Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain F residue 363 CYS Chi-restraints excluded: chain F residue 577 LEU 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 E residue 49 ILE Chi-restraints excluded: chain E residue 51 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 23 optimal weight: 0.0010 chunk 174 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 497 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5556 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23856 Z= 0.281 Angle : 0.575 13.317 32227 Z= 0.299 Chirality : 0.041 0.232 3618 Planarity : 0.004 0.077 4130 Dihedral : 4.259 36.310 3140 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.93 % Allowed : 16.99 % Favored : 81.08 % 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: -0.25 (0.16), residues: 2869 helix: 0.81 (0.13), residues: 1738 sheet: -1.42 (0.61), residues: 64 loop : -1.71 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP I 72 HIS 0.021 0.001 HIS F 382 PHE 0.028 0.002 PHE F 388 TYR 0.027 0.001 TYR C 83 ARG 0.008 0.000 ARG J 171 ********************** 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 348 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 298 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 50 MET cc_start: 0.4916 (mmt) cc_final: 0.1955 (ptm) REVERT: B 26 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7611 (mpp) REVERT: B 86 MET cc_start: 0.7933 (mmt) cc_final: 0.7594 (mmt) REVERT: B 567 ASN cc_start: 0.7686 (p0) cc_final: 0.7284 (p0) REVERT: D 53 ASP cc_start: 0.7475 (m-30) cc_final: 0.6943 (t70) REVERT: F 399 ASN cc_start: 0.8339 (m-40) cc_final: 0.7798 (t0) REVERT: F 408 GLU cc_start: 0.6529 (pt0) cc_final: 0.6118 (mt-10) REVERT: F 530 ASN cc_start: 0.7376 (m-40) cc_final: 0.6977 (m-40) REVERT: J 567 ASP cc_start: 0.7966 (t0) cc_final: 0.7629 (t0) REVERT: J 618 ARG cc_start: 0.7444 (mtm110) cc_final: 0.7114 (ttp80) outliers start: 50 outliers final: 45 residues processed: 331 average time/residue: 0.3458 time to fit residues: 182.7895 Evaluate side-chains 341 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 295 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 89 ARG 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 294 MET Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 505 ILE 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 712 ASN Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain F residue 363 CYS Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 577 LEU 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 E residue 49 ILE Chi-restraints excluded: chain E residue 51 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 231 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 198 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 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 = 0.4465 r_free = 0.4465 target = 0.210434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.166563 restraints weight = 29601.988| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.09 r_work: 0.3771 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23856 Z= 0.206 Angle : 0.546 12.900 32227 Z= 0.283 Chirality : 0.039 0.223 3618 Planarity : 0.004 0.076 4130 Dihedral : 4.194 34.210 3140 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.73 % Allowed : 17.03 % Favored : 81.23 % 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: 1735 sheet: -1.41 (0.58), residues: 73 loop : -1.69 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP I 72 HIS 0.025 0.001 HIS F 382 PHE 0.026 0.001 PHE B 112 TYR 0.025 0.001 TYR C 83 ARG 0.008 0.000 ARG J 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5710.35 seconds wall clock time: 105 minutes 21.26 seconds (6321.26 seconds total)