Starting phenix.real_space_refine on Mon Jul 6 16:00:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z7r_14535/07_2026/7z7r_14535.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z7r_14535/07_2026/7z7r_14535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z7r_14535/07_2026/7z7r_14535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z7r_14535/07_2026/7z7r_14535.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z7r_14535/07_2026/7z7r_14535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z7r_14535/07_2026/7z7r_14535.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z7r_14535/07_2026/7z7r_14535.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z7r_14535/07_2026/7z7r_14535.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 3 5.49 5 S 267 5.16 5 C 24182 2.51 5 N 6222 2.21 5 O 6545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37252 Number of models: 1 Model: "" Number of chains: 21 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7027 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4736 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 548} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1656 Classifications: {'peptide': 208} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 193} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2529 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 894 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4627 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 586} Chain breaks: 1 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3563 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 450} Chain breaks: 2 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 67.987 59.921 187.891 1.00 31.95 S ATOM 2741 SG CYS F 357 71.589 59.357 192.301 1.00 60.22 S ATOM 3062 SG CYS F 398 65.737 56.077 192.749 1.00 54.73 S ATOM 2697 SG CYS F 351 70.042 53.562 189.061 1.00 33.90 S ATOM 4054 SG CYS E 92 78.260 50.402 208.658 1.00 68.10 S ATOM 4088 SG CYS E 97 78.596 51.276 212.045 1.00 53.60 S ATOM 4366 SG CYS E 133 73.123 50.045 208.413 1.00 66.31 S ATOM 4392 SG CYS E 137 72.397 50.867 211.788 1.00 82.18 S ATOM 5476 SG CYS G 114 79.265 66.162 170.859 1.00 47.02 S ATOM 5416 SG CYS G 105 84.790 69.216 172.664 1.00 62.92 S ATOM 5436 SG CYS G 108 84.967 63.747 169.259 1.00 34.29 S ATOM 5830 SG CYS G 156 72.950 58.389 175.307 1.00 31.54 S ATOM 5811 SG CYS G 153 78.784 57.210 178.236 1.00 62.34 S ATOM 5859 SG CYS G 159 75.828 52.582 174.705 1.00 51.39 S ATOM 6207 SG CYS G 203 78.108 57.729 171.666 1.00 56.45 S ATOM 6432 SG CYS G 230 74.622 50.009 150.219 1.00 41.15 S ATOM 6717 SG CYS G 265 74.397 46.181 155.529 1.00 52.92 S ATOM 6480 SG CYS G 237 69.265 49.918 153.465 1.00 41.66 S ATOM 6456 SG CYS G 233 71.190 44.501 150.248 1.00 80.99 S ATOM 4877 SG CYS G 36 66.230 59.527 177.722 1.00 38.20 S ATOM 4953 SG CYS G 47 68.126 62.737 178.351 1.00 33.05 S ATOM 4979 SG CYS G 50 62.390 64.725 178.536 1.00 54.60 S ATOM 5128 SG CYS G 69 61.837 61.073 177.973 1.00 40.35 S ATOM 17324 SG CYS B 129 90.788 93.665 147.268 1.00 38.24 S ATOM 16821 SG CYS B 64 96.158 97.070 149.031 1.00 38.82 S ATOM 16815 SG CYS B 63 90.678 99.315 151.088 1.00 60.66 S ATOM 17541 SG CYS B 158 92.531 93.546 153.277 1.00 62.62 S ATOM 18872 SG CYS I 102 90.831 87.304 159.132 1.00 36.25 S ATOM 18847 SG CYS I 99 96.308 85.919 155.536 1.00 48.08 S ATOM 18890 SG CYS I 105 94.860 82.616 160.903 1.00 91.54 S ATOM 18605 SG CYS I 70 91.035 82.012 155.634 1.00 38.72 S ATOM 18919 SG CYS I 109 95.474 76.820 166.808 1.00 69.31 S ATOM 18582 SG CYS I 66 93.537 76.213 160.685 1.00 69.56 S ATOM 18542 SG CYS I 60 97.331 71.585 163.174 1.00 39.17 S ATOM 18560 SG CYS I 63 91.102 72.480 165.405 1.00 46.86 S Time building chain proxies: 7.87, per 1000 atoms: 0.21 Number of scatterers: 37252 At special positions: 0 Unit cell: (157.3, 220.22, 239.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 267 16.00 P 3 15.00 O 6545 8.00 N 6222 7.00 C 24182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8680 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 52.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 271 through 274 No H-bonds generated for 'chain 'F' and resid 271 through 274' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 419 No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 35 through 47 Processing helix chain 'E' and resid 53 through 62 Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 98 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.851A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 273 through 276 No H-bonds generated for 'chain 'G' and resid 273 through 276' Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.294A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 764 through 770 removed outlier: 5.288A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS G 769 " --> pdb=" O GLN G 765 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 829 removed outlier: 4.304A pdb=" N ARG G 829 " --> pdb=" O GLU G 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 825 through 829' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.993A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 4.832A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 8.804A pdb=" N THR C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N LYS C 187 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ALA C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 376 through 399 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 432 removed outlier: 4.449A pdb=" N THR C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 575 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.435A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'H' and resid 6 through 44 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.515A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.044A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 322 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 66 through 89 Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'L' and resid 4 through 21 removed outlier: 4.394A pdb=" N ILE L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.505A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 259 through 268 removed outlier: 4.624A pdb=" N VAL L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 275 Processing helix chain 'L' and resid 277 through 299 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 519 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 548 Processing helix chain 'L' and resid 550 through 562 removed outlier: 5.184A pdb=" N ARG L 562 " --> pdb=" O TRP L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 584 Proline residue: L 572 - end of helix Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 28 through 50 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 157 removed outlier: 4.856A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 200 Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 491 through 502 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 3.663A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.332A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.120A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.060A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 56 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 112 removed outlier: 5.435A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1712 hydrogen bonds defined for protein. 5136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15983 1.42 - 1.64: 21712 1.64 - 1.86: 410 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 38197 Sorted by residual: bond pdb=" CG PRO M 61 " pdb=" CD PRO M 61 " ideal model delta sigma weight residual 1.512 1.386 0.126 2.70e-02 1.37e+03 2.19e+01 bond pdb=" CB PRO M 61 " pdb=" CG PRO M 61 " ideal model delta sigma weight residual 1.506 1.653 -0.147 3.90e-02 6.57e+02 1.42e+01 bond pdb=" O13 3PE C 701 " pdb=" P 3PE C 701 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.53e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" O11 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.644 1.594 0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 38192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 51435 3.49 - 6.99: 364 6.99 - 10.48: 79 10.48 - 13.98: 15 13.98 - 17.47: 8 Bond angle restraints: 51901 Sorted by residual: angle pdb=" N PRO M 61 " pdb=" CD PRO M 61 " pdb=" CG PRO M 61 " ideal model delta sigma weight residual 103.80 93.50 10.30 1.20e+00 6.94e-01 7.37e+01 angle pdb=" CA PRO M 61 " pdb=" N PRO M 61 " pdb=" CD PRO M 61 " ideal model delta sigma weight residual 111.50 101.53 9.97 1.40e+00 5.10e-01 5.08e+01 angle pdb=" CB MET C 387 " pdb=" CG MET C 387 " pdb=" SD MET C 387 " ideal model delta sigma weight residual 112.70 130.17 -17.47 3.00e+00 1.11e-01 3.39e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.35 12.46 2.21e+00 2.05e-01 3.18e+01 angle pdb=" CB MET H 281 " pdb=" CG MET H 281 " pdb=" SD MET H 281 " ideal model delta sigma weight residual 112.70 129.52 -16.82 3.00e+00 1.11e-01 3.14e+01 ... (remaining 51896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 21495 33.84 - 67.68: 800 67.68 - 101.52: 54 101.52 - 135.36: 0 135.36 - 169.20: 1 Dihedral angle restraints: 22350 sinusoidal: 8781 harmonic: 13569 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 133.23 46.77 0 5.00e+00 4.00e-02 8.75e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 88.39 169.20 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA TRP G 668 " pdb=" C TRP G 668 " pdb=" N THR G 669 " pdb=" CA THR G 669 " ideal model delta harmonic sigma weight residual 180.00 146.13 33.87 0 5.00e+00 4.00e-02 4.59e+01 ... (remaining 22347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.247: 5796 4.247 - 8.495: 0 8.495 - 12.742: 0 12.742 - 16.990: 0 16.990 - 21.237: 28 Chirality restraints: 5824 Sorted by residual: chirality pdb="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.68 21.24 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 G1001 " pdb=" S1 SF4 G1001 " pdb=" S2 SF4 G1001 " pdb=" S4 SF4 G1001 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.16 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.60 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5821 not shown) Planarity restraints: 6532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C VAL N 63 " 0.057 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.022 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER G 763 " -0.051 5.00e-02 4.00e+02 7.85e-02 9.85e+00 pdb=" N PRO G 764 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO G 764 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 764 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 64 " 0.052 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO N 65 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO N 65 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO N 65 " 0.044 5.00e-02 4.00e+02 ... (remaining 6529 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 6384 2.77 - 3.30: 35909 3.30 - 3.83: 67854 3.83 - 4.37: 78879 4.37 - 4.90: 134957 Nonbonded interactions: 323983 Sorted by model distance: nonbonded pdb=" O ALA L 256 " pdb=" OG1 THR L 260 " model vdw 2.232 3.040 nonbonded pdb=" O GLU C 276 " pdb=" ND2 ASN C 283 " model vdw 2.255 3.120 nonbonded pdb=" O ILE M 421 " pdb=" OG SER M 425 " model vdw 2.266 3.040 nonbonded pdb=" O TRP M 499 " pdb=" OG SER M 503 " model vdw 2.266 3.040 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.267 3.040 ... (remaining 323978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.680 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 35.700 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.005 0.147 38233 Z= 0.196 Angle : 0.859 17.469 51994 Z= 0.423 Chirality : 1.466 21.237 5824 Planarity : 0.006 0.078 6532 Dihedral : 16.836 169.201 13670 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.72 % Favored : 97.26 % Rotamer: Outliers : 0.41 % Allowed : 23.91 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.11), residues: 4710 helix: 0.10 (0.09), residues: 2641 sheet: -0.40 (0.29), residues: 329 loop : -0.96 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 293 TYR 0.046 0.002 TYR C 322 PHE 0.050 0.002 PHE N 241 TRP 0.025 0.001 TRP L 143 HIS 0.008 0.001 HIS M 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (38197) covalent geometry : angle 0.84603 / 0.42 (51901) hydrogen bonds : bond 0.05290 / 3.52 ( 1712) hydrogen bonds : angle 4.80132 / 3.42 ( 5136) metal coordination : bond 0.05322 / 3.42 ( 36) metal coordination : angle 3.55310 / 2.56 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 495 time to evaluate : 1.233 Fit side-chains REVERT: B 22 GLN cc_start: 0.7719 (mp10) cc_final: 0.7517 (mp10) REVERT: B 54 ILE cc_start: 0.8876 (mt) cc_final: 0.8669 (tp) REVERT: I 39 TYR cc_start: 0.8781 (t80) cc_final: 0.8521 (t80) REVERT: H 284 LEU cc_start: 0.8913 (tp) cc_final: 0.8671 (mp) REVERT: L 219 THR cc_start: 0.7233 (p) cc_final: 0.6814 (p) REVERT: M 11 PHE cc_start: 0.8034 (m-10) cc_final: 0.7508 (m-10) REVERT: M 395 THR cc_start: 0.8705 (t) cc_final: 0.8468 (t) REVERT: K 72 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8468 (mt-10) outliers start: 16 outliers final: 6 residues processed: 505 average time/residue: 0.1951 time to fit residues: 167.6361 Evaluate side-chains 446 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 440 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain N residue 140 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 218 ASN G 513 GLN B 92 GLN I 13 GLN H 45 ASN H 170 GLN H 208 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 HIS K 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.071904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063551 restraints weight = 109589.789| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.13 r_work: 0.3247 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.265 38233 Z= 0.399 Angle : 2.511 50.917 51994 Z= 1.442 Chirality : 0.436 6.430 5824 Planarity : 0.004 0.062 6532 Dihedral : 5.766 169.984 5244 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.88 % Allowed : 22.08 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.12), residues: 4710 helix: 0.86 (0.10), residues: 2667 sheet: -0.53 (0.28), residues: 338 loop : -0.75 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 293 TYR 0.022 0.001 TYR M 435 PHE 0.023 0.001 PHE L 341 TRP 0.018 0.001 TRP M 143 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01155 / 0.40 (38197) covalent geometry : angle 2.19306 / 1.44 (51901) hydrogen bonds : bond 0.04581 / 3.07 ( 1712) hydrogen bonds : angle 4.28828 / 3.05 ( 5136) metal coordination : bond 0.04180 / 2.91 ( 36) metal coordination : angle 28.98864 / 20.85 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 463 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: F 309 MET cc_start: 0.8386 (mmm) cc_final: 0.8161 (mmm) REVERT: G 119 MET cc_start: 0.9116 (mmt) cc_final: 0.8873 (mmt) REVERT: G 631 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8381 (ttp-110) REVERT: C 285 MET cc_start: 0.9065 (tpp) cc_final: 0.8536 (ttm) REVERT: C 322 TYR cc_start: 0.8690 (t80) cc_final: 0.8465 (t80) REVERT: B 22 GLN cc_start: 0.8007 (mp10) cc_final: 0.7734 (mp10) REVERT: B 170 MET cc_start: 0.8410 (mtm) cc_final: 0.8072 (mtm) REVERT: A 44 ARG cc_start: 0.7577 (mtp180) cc_final: 0.7342 (mtp180) REVERT: A 74 PHE cc_start: 0.8811 (m-10) cc_final: 0.8568 (m-10) REVERT: L 598 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8524 (ttp) REVERT: M 323 MET cc_start: 0.8017 (mmt) cc_final: 0.7626 (mmt) REVERT: M 338 TYR cc_start: 0.8161 (m-10) cc_final: 0.7693 (m-10) REVERT: M 395 THR cc_start: 0.8667 (t) cc_final: 0.8410 (t) REVERT: N 139 LEU cc_start: 0.8782 (mt) cc_final: 0.8558 (mm) REVERT: N 174 MET cc_start: 0.8973 (mtt) cc_final: 0.8647 (mtt) REVERT: N 334 LEU cc_start: 0.8934 (tp) cc_final: 0.8726 (tt) REVERT: J 85 ARG cc_start: 0.8857 (mtm180) cc_final: 0.8560 (mtm110) REVERT: J 115 ASN cc_start: 0.8410 (t0) cc_final: 0.7816 (p0) outliers start: 73 outliers final: 33 residues processed: 515 average time/residue: 0.1972 time to fit residues: 171.6448 Evaluate side-chains 470 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 435 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 303 LYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 55 optimal weight: 0.9990 chunk 218 optimal weight: 0.2980 chunk 159 optimal weight: 4.9990 chunk 380 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 353 optimal weight: 8.9990 chunk 382 optimal weight: 5.9990 chunk 457 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 362 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 137 HIS G 218 ASN C 359 HIS H 45 ASN H 208 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.071114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062763 restraints weight = 110071.783| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.15 r_work: 0.3227 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.249 38233 Z= 0.393 Angle : 2.505 50.774 51994 Z= 1.438 Chirality : 0.440 6.419 5824 Planarity : 0.004 0.063 6532 Dihedral : 5.499 170.861 5234 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.73 % Allowed : 21.16 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.12), residues: 4710 helix: 1.22 (0.10), residues: 2663 sheet: -0.31 (0.30), residues: 321 loop : -0.66 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.021 0.001 TYR L 428 PHE 0.027 0.001 PHE N 140 TRP 0.017 0.001 TRP M 143 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01140 / 0.39 (38197) covalent geometry : angle 2.18355 / 1.44 (51901) hydrogen bonds : bond 0.04554 / 3.06 ( 1712) hydrogen bonds : angle 4.19359 / 2.99 ( 5136) metal coordination : bond 0.02725 / 1.81 ( 36) metal coordination : angle 29.11235 / 20.92 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 448 time to evaluate : 1.364 Fit side-chains REVERT: G 70 MET cc_start: 0.9200 (mmm) cc_final: 0.8598 (mmm) REVERT: G 119 MET cc_start: 0.9030 (mmt) cc_final: 0.8752 (mmp) REVERT: G 288 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7774 (mtt90) REVERT: G 631 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8371 (ttp-110) REVERT: C 285 MET cc_start: 0.9074 (tpp) cc_final: 0.8656 (ttm) REVERT: C 571 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8324 (tp40) REVERT: B 22 GLN cc_start: 0.8020 (mp10) cc_final: 0.7689 (mp10) REVERT: I 13 GLN cc_start: 0.8999 (mp-120) cc_final: 0.8459 (mp10) REVERT: H 118 PHE cc_start: 0.7823 (t80) cc_final: 0.7479 (t80) REVERT: H 122 MET cc_start: 0.8584 (mmp) cc_final: 0.8338 (mmm) REVERT: H 284 LEU cc_start: 0.9004 (tp) cc_final: 0.8794 (tp) REVERT: A 44 ARG cc_start: 0.7579 (mtp180) cc_final: 0.7203 (mtp180) REVERT: A 73 MET cc_start: 0.9067 (tmm) cc_final: 0.8778 (tmm) REVERT: A 74 PHE cc_start: 0.8906 (m-10) cc_final: 0.8680 (m-10) REVERT: L 598 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8565 (ttp) REVERT: M 121 MET cc_start: 0.8095 (mpp) cc_final: 0.7216 (mpp) REVERT: M 174 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8185 (t80) REVERT: M 323 MET cc_start: 0.8016 (mmt) cc_final: 0.7600 (mmt) REVERT: M 338 TYR cc_start: 0.8203 (m-10) cc_final: 0.7891 (m-10) REVERT: M 395 THR cc_start: 0.8628 (t) cc_final: 0.8351 (t) REVERT: K 46 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.7917 (t80) REVERT: J 73 MET cc_start: 0.8155 (mmm) cc_final: 0.7498 (mmm) REVERT: J 115 ASN cc_start: 0.8501 (t0) cc_final: 0.7819 (p0) outliers start: 106 outliers final: 59 residues processed: 525 average time/residue: 0.1961 time to fit residues: 174.8645 Evaluate side-chains 498 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 433 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 140 PHE Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 269 ILE Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 386 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 447 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 468 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 357 optimal weight: 10.0000 chunk 437 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 100 ASN G 218 ASN G 299 GLN H 138 ASN H 208 HIS A 47 ASN ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 406 HIS ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.070083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.061724 restraints weight = 110579.151| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.11 r_work: 0.3200 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 38233 Z= 0.401 Angle : 2.516 50.750 51994 Z= 1.441 Chirality : 0.439 6.398 5824 Planarity : 0.004 0.062 6532 Dihedral : 5.510 171.133 5234 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.14 % Allowed : 21.36 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.12), residues: 4710 helix: 1.35 (0.10), residues: 2663 sheet: -0.29 (0.30), residues: 332 loop : -0.58 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 293 TYR 0.025 0.001 TYR L 428 PHE 0.026 0.001 PHE N 140 TRP 0.016 0.001 TRP M 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01154 / 0.40 (38197) covalent geometry : angle 2.19067 / 1.44 (51901) hydrogen bonds : bond 0.04708 / 3.16 ( 1712) hydrogen bonds : angle 4.21674 / 3.00 ( 5136) metal coordination : bond 0.02388 / 1.63 ( 36) metal coordination : angle 29.32307 / 21.09 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 441 time to evaluate : 1.062 Fit side-chains REVERT: E 121 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.7882 (p) REVERT: G 70 MET cc_start: 0.9208 (mmm) cc_final: 0.8710 (mmm) REVERT: G 288 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7783 (mtt90) REVERT: G 292 PHE cc_start: 0.8665 (m-80) cc_final: 0.8408 (m-10) REVERT: G 631 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.8404 (ttp-110) REVERT: C 285 MET cc_start: 0.9074 (tpp) cc_final: 0.8699 (ttm) REVERT: C 571 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8375 (tp40) REVERT: B 22 GLN cc_start: 0.8012 (mp10) cc_final: 0.7672 (mp10) REVERT: I 13 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8785 (mp10) REVERT: H 67 MET cc_start: 0.8542 (mtt) cc_final: 0.8342 (mtt) REVERT: H 118 PHE cc_start: 0.7967 (t80) cc_final: 0.7443 (t80) REVERT: H 284 LEU cc_start: 0.9061 (tp) cc_final: 0.8825 (tp) REVERT: H 312 ASN cc_start: 0.9293 (OUTLIER) cc_final: 0.9058 (t0) REVERT: A 73 MET cc_start: 0.9114 (tmm) cc_final: 0.8603 (tmm) REVERT: A 74 PHE cc_start: 0.8958 (m-10) cc_final: 0.8743 (m-10) REVERT: L 134 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8313 (t70) REVERT: L 568 MET cc_start: 0.7423 (mmp) cc_final: 0.7138 (mmm) REVERT: L 598 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8599 (ttp) REVERT: M 121 MET cc_start: 0.8117 (mpp) cc_final: 0.7764 (mpt) REVERT: M 174 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8472 (t80) REVERT: M 323 MET cc_start: 0.8073 (mmt) cc_final: 0.7752 (mmt) REVERT: K 46 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.7902 (t80) REVERT: J 73 MET cc_start: 0.8270 (mmm) cc_final: 0.8015 (mmm) REVERT: J 115 ASN cc_start: 0.8449 (t0) cc_final: 0.7831 (p0) outliers start: 122 outliers final: 82 residues processed: 532 average time/residue: 0.1971 time to fit residues: 176.9376 Evaluate side-chains 513 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 421 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 140 PHE Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 269 ILE Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 29 optimal weight: 5.9990 chunk 390 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 393 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 382 optimal weight: 9.9990 chunk 377 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 218 ASN H 208 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.069291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.060959 restraints weight = 110695.135| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.13 r_work: 0.3181 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 38233 Z= 0.407 Angle : 2.522 50.768 51994 Z= 1.442 Chirality : 0.440 6.399 5824 Planarity : 0.004 0.061 6532 Dihedral : 5.557 171.826 5234 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.96 % Allowed : 21.21 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.12), residues: 4710 helix: 1.37 (0.10), residues: 2660 sheet: -0.31 (0.30), residues: 330 loop : -0.56 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 198 TYR 0.022 0.002 TYR L 428 PHE 0.027 0.001 PHE N 140 TRP 0.016 0.001 TRP M 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01163 / 0.41 (38197) covalent geometry : angle 2.19408 / 1.44 (51901) hydrogen bonds : bond 0.04871 / 3.27 ( 1712) hydrogen bonds : angle 4.25762 / 3.03 ( 5136) metal coordination : bond 0.02330 / 1.60 ( 36) metal coordination : angle 29.46373 / 21.17 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 427 time to evaluate : 1.384 Fit side-chains REVERT: F 182 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: E 121 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.7902 (p) REVERT: G 70 MET cc_start: 0.9223 (mmm) cc_final: 0.8792 (mmm) REVERT: G 119 MET cc_start: 0.9025 (mmt) cc_final: 0.8734 (mmp) REVERT: G 288 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7810 (mtt90) REVERT: G 292 PHE cc_start: 0.8622 (m-80) cc_final: 0.8343 (m-10) REVERT: G 631 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.8425 (ttp-110) REVERT: G 750 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.7697 (ptt90) REVERT: C 285 MET cc_start: 0.9080 (tpp) cc_final: 0.8675 (ttm) REVERT: C 571 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8370 (tp40) REVERT: B 22 GLN cc_start: 0.7979 (mp10) cc_final: 0.7613 (mp10) REVERT: I 13 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8781 (mp10) REVERT: H 67 MET cc_start: 0.8595 (mtt) cc_final: 0.8374 (mtt) REVERT: H 118 PHE cc_start: 0.8038 (t80) cc_final: 0.7591 (t80) REVERT: H 284 LEU cc_start: 0.9144 (tp) cc_final: 0.8938 (tp) REVERT: H 312 ASN cc_start: 0.9319 (OUTLIER) cc_final: 0.9111 (t0) REVERT: A 73 MET cc_start: 0.9171 (tmm) cc_final: 0.8673 (tmm) REVERT: L 354 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7575 (mp) REVERT: L 568 MET cc_start: 0.7444 (mmp) cc_final: 0.7159 (mmm) REVERT: L 598 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8570 (ttp) REVERT: M 121 MET cc_start: 0.8141 (mpp) cc_final: 0.7792 (mpt) REVERT: M 174 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8500 (t80) REVERT: M 323 MET cc_start: 0.8199 (mmt) cc_final: 0.7884 (mmt) REVERT: M 364 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8364 (tm-30) REVERT: N 63 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8137 (p) REVERT: N 103 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: N 294 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7889 (mp) REVERT: K 46 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7982 (t80) REVERT: J 73 MET cc_start: 0.8357 (mmm) cc_final: 0.8062 (mmm) REVERT: J 115 ASN cc_start: 0.8423 (t0) cc_final: 0.7809 (p0) outliers start: 154 outliers final: 97 residues processed: 548 average time/residue: 0.1933 time to fit residues: 179.9679 Evaluate side-chains 527 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 415 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 140 PHE Chi-restraints excluded: chain N residue 186 PHE Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 461 optimal weight: 30.0000 chunk 159 optimal weight: 20.0000 chunk 191 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 308 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 394 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 218 ASN G 901 HIS H 208 HIS ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 241 HIS ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 305 HIS J 75 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.069071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.060744 restraints weight = 110078.787| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.12 r_work: 0.3173 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 38233 Z= 0.408 Angle : 2.525 50.779 51994 Z= 1.443 Chirality : 0.439 6.399 5824 Planarity : 0.004 0.061 6532 Dihedral : 5.589 172.244 5234 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.09 % Allowed : 21.80 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.12), residues: 4710 helix: 1.38 (0.10), residues: 2660 sheet: -0.39 (0.30), residues: 330 loop : -0.54 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 16 TYR 0.024 0.002 TYR K 62 PHE 0.027 0.001 PHE N 140 TRP 0.017 0.001 TRP M 122 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01166 / 0.41 (38197) covalent geometry : angle 2.19693 / 1.44 (51901) hydrogen bonds : bond 0.04906 / 3.29 ( 1712) hydrogen bonds : angle 4.27823 / 3.05 ( 5136) metal coordination : bond 0.02285 / 1.57 ( 36) metal coordination : angle 29.53355 / 21.21 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 418 time to evaluate : 1.450 Fit side-chains REVERT: F 36 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8548 (tp30) REVERT: F 182 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8343 (tm-30) REVERT: E 121 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.7907 (p) REVERT: G 70 MET cc_start: 0.9216 (mmm) cc_final: 0.8724 (mmm) REVERT: G 119 MET cc_start: 0.8939 (mmt) cc_final: 0.8649 (mmp) REVERT: G 187 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: G 288 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7764 (mtt90) REVERT: G 292 PHE cc_start: 0.8606 (m-80) cc_final: 0.8329 (m-10) REVERT: G 631 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.8443 (ttp-110) REVERT: C 285 MET cc_start: 0.9145 (tpp) cc_final: 0.8709 (ttm) REVERT: C 571 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8359 (tp40) REVERT: B 22 GLN cc_start: 0.7967 (mp10) cc_final: 0.7597 (mp10) REVERT: B 193 TYR cc_start: 0.7831 (m-10) cc_final: 0.7575 (m-10) REVERT: I 13 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8792 (mp10) REVERT: H 66 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8567 (ptmm) REVERT: H 67 MET cc_start: 0.8582 (mtt) cc_final: 0.8375 (mtt) REVERT: H 118 PHE cc_start: 0.7999 (t80) cc_final: 0.7432 (t80) REVERT: H 170 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8191 (mt0) REVERT: H 312 ASN cc_start: 0.9340 (OUTLIER) cc_final: 0.9129 (t0) REVERT: A 73 MET cc_start: 0.9146 (tmm) cc_final: 0.8662 (tmm) REVERT: A 74 PHE cc_start: 0.9053 (m-10) cc_final: 0.8847 (m-10) REVERT: L 354 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7576 (mp) REVERT: L 377 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7325 (tt) REVERT: L 568 MET cc_start: 0.7450 (mmp) cc_final: 0.7164 (mmm) REVERT: L 598 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8513 (ttp) REVERT: M 63 TRP cc_start: 0.7956 (OUTLIER) cc_final: 0.6816 (m100) REVERT: M 121 MET cc_start: 0.8137 (mpp) cc_final: 0.7643 (mpt) REVERT: M 174 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8478 (t80) REVERT: M 323 MET cc_start: 0.8179 (mmt) cc_final: 0.7885 (mmt) REVERT: M 364 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8391 (tm-30) REVERT: N 103 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: K 46 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.7975 (t80) REVERT: J 73 MET cc_start: 0.8401 (mmm) cc_final: 0.8082 (mmm) REVERT: J 98 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8166 (pt) REVERT: J 115 ASN cc_start: 0.8391 (t0) cc_final: 0.7733 (p0) outliers start: 159 outliers final: 101 residues processed: 542 average time/residue: 0.2007 time to fit residues: 184.9260 Evaluate side-chains 526 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 406 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 667 ASP Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 170 GLN Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 63 TRP Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 140 PHE Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 352 optimal weight: 3.9990 chunk 291 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 276 optimal weight: 20.0000 chunk 274 optimal weight: 20.0000 chunk 334 optimal weight: 20.0000 chunk 428 optimal weight: 7.9990 chunk 447 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 469 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 218 ASN H 208 HIS ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.068455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.060181 restraints weight = 110475.011| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.11 r_work: 0.3161 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 38233 Z= 0.417 Angle : 2.533 50.783 51994 Z= 1.446 Chirality : 0.440 6.402 5824 Planarity : 0.004 0.061 6532 Dihedral : 5.714 172.648 5234 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.30 % Allowed : 21.75 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.12), residues: 4710 helix: 1.33 (0.10), residues: 2662 sheet: -0.48 (0.30), residues: 327 loop : -0.57 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 16 TYR 0.020 0.002 TYR N 424 PHE 0.028 0.002 PHE N 140 TRP 0.016 0.001 TRP M 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01181 / 0.42 (38197) covalent geometry : angle 2.20330 / 1.44 (51901) hydrogen bonds : bond 0.05079 / 3.41 ( 1712) hydrogen bonds : angle 4.33984 / 3.09 ( 5136) metal coordination : bond 0.02358 / 1.61 ( 36) metal coordination : angle 29.62551 / 21.28 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 424 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: F 36 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8487 (tp30) REVERT: F 182 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: G 70 MET cc_start: 0.9212 (mmm) cc_final: 0.8709 (mmm) REVERT: G 119 MET cc_start: 0.8939 (mmt) cc_final: 0.8664 (mmp) REVERT: G 187 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8571 (pm20) REVERT: G 288 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7824 (mtt90) REVERT: G 292 PHE cc_start: 0.8642 (m-80) cc_final: 0.8366 (m-10) REVERT: G 631 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8457 (ttp-110) REVERT: C 285 MET cc_start: 0.9152 (tpp) cc_final: 0.8660 (ttm) REVERT: C 571 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8397 (tp40) REVERT: B 22 GLN cc_start: 0.7928 (mp10) cc_final: 0.7558 (mp10) REVERT: B 193 TYR cc_start: 0.7908 (m-10) cc_final: 0.7652 (m-10) REVERT: I 13 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8780 (mp10) REVERT: H 32 MET cc_start: 0.8757 (tpp) cc_final: 0.8535 (tpt) REVERT: H 67 MET cc_start: 0.8609 (mtt) cc_final: 0.8355 (mtt) REVERT: H 118 PHE cc_start: 0.8075 (t80) cc_final: 0.7572 (t80) REVERT: H 170 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: H 284 LEU cc_start: 0.9019 (tp) cc_final: 0.8773 (mt) REVERT: H 312 ASN cc_start: 0.9348 (OUTLIER) cc_final: 0.9148 (t0) REVERT: A 73 MET cc_start: 0.9230 (tmm) cc_final: 0.8742 (tmm) REVERT: A 74 PHE cc_start: 0.9197 (m-10) cc_final: 0.8989 (m-10) REVERT: L 354 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7651 (mp) REVERT: L 377 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7296 (tt) REVERT: L 568 MET cc_start: 0.7503 (mmp) cc_final: 0.7235 (mmm) REVERT: L 598 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8523 (ttp) REVERT: M 63 TRP cc_start: 0.7918 (OUTLIER) cc_final: 0.6803 (m100) REVERT: M 121 MET cc_start: 0.8165 (mpp) cc_final: 0.7353 (mpp) REVERT: M 174 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8540 (t80) REVERT: M 323 MET cc_start: 0.8203 (mmt) cc_final: 0.7895 (mmt) REVERT: M 364 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8489 (tm-30) REVERT: N 75 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8067 (tp) REVERT: N 103 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: K 31 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8582 (ttp) REVERT: K 46 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7976 (t80) REVERT: J 73 MET cc_start: 0.8387 (mmm) cc_final: 0.8086 (mmm) REVERT: J 98 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8164 (pt) REVERT: J 115 ASN cc_start: 0.8401 (t0) cc_final: 0.7760 (p0) outliers start: 167 outliers final: 112 residues processed: 556 average time/residue: 0.1946 time to fit residues: 184.6532 Evaluate side-chains 539 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 408 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 170 GLN Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 63 TRP Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 140 PHE Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 235 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 460 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 218 ASN H 208 HIS ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.068906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.060713 restraints weight = 109004.565| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.09 r_work: 0.3175 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 38233 Z= 0.403 Angle : 2.529 50.780 51994 Z= 1.444 Chirality : 0.439 6.398 5824 Planarity : 0.004 0.061 6532 Dihedral : 5.704 173.087 5234 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.91 % Allowed : 22.55 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.12), residues: 4710 helix: 1.36 (0.10), residues: 2663 sheet: -0.43 (0.29), residues: 330 loop : -0.55 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 16 TYR 0.021 0.002 TYR L 428 PHE 0.028 0.001 PHE N 140 TRP 0.019 0.001 TRP M 122 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01159 / 0.40 (38197) covalent geometry : angle 2.20031 / 1.44 (51901) hydrogen bonds : bond 0.04898 / 3.29 ( 1712) hydrogen bonds : angle 4.29814 / 3.07 ( 5136) metal coordination : bond 0.02180 / 1.50 ( 36) metal coordination : angle 29.57943 / 21.23 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 422 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 36 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8458 (tp30) REVERT: F 182 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: F 358 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8010 (ttp-110) REVERT: G 70 MET cc_start: 0.9183 (mmm) cc_final: 0.8792 (mmm) REVERT: G 119 MET cc_start: 0.8923 (mmt) cc_final: 0.8668 (mmp) REVERT: G 187 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8558 (pm20) REVERT: G 292 PHE cc_start: 0.8647 (m-80) cc_final: 0.8372 (m-10) REVERT: G 631 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.8454 (ttp-110) REVERT: C 285 MET cc_start: 0.9158 (tpp) cc_final: 0.8653 (ttm) REVERT: C 571 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8382 (tp40) REVERT: B 22 GLN cc_start: 0.7899 (mp10) cc_final: 0.7534 (mp10) REVERT: B 193 TYR cc_start: 0.7891 (m-10) cc_final: 0.7637 (m-10) REVERT: I 13 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8793 (mp10) REVERT: I 27 LYS cc_start: 0.8043 (tppt) cc_final: 0.7645 (tppt) REVERT: H 32 MET cc_start: 0.8751 (tpp) cc_final: 0.8534 (tpt) REVERT: H 66 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8505 (ptmm) REVERT: H 118 PHE cc_start: 0.8024 (t80) cc_final: 0.7556 (t80) REVERT: H 122 MET cc_start: 0.8690 (mmp) cc_final: 0.8381 (mmm) REVERT: H 170 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: H 284 LEU cc_start: 0.9060 (tp) cc_final: 0.8810 (mt) REVERT: H 312 ASN cc_start: 0.9352 (OUTLIER) cc_final: 0.9147 (t0) REVERT: A 73 MET cc_start: 0.9215 (tmm) cc_final: 0.8762 (tmm) REVERT: L 354 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7621 (mp) REVERT: L 377 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7291 (tt) REVERT: L 568 MET cc_start: 0.7562 (mmp) cc_final: 0.7276 (mmm) REVERT: L 598 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8530 (ttp) REVERT: M 63 TRP cc_start: 0.7836 (OUTLIER) cc_final: 0.6671 (m100) REVERT: M 121 MET cc_start: 0.7957 (mpp) cc_final: 0.7599 (mpt) REVERT: M 174 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8521 (t80) REVERT: M 323 MET cc_start: 0.8180 (mmt) cc_final: 0.7909 (mmt) REVERT: M 364 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8512 (tm-30) REVERT: N 25 MET cc_start: 0.9063 (tpp) cc_final: 0.8833 (tpp) REVERT: N 103 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: K 46 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.7916 (t80) REVERT: J 73 MET cc_start: 0.8412 (mmm) cc_final: 0.8101 (mmm) REVERT: J 94 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8258 (mm) REVERT: J 98 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8195 (pt) REVERT: J 115 ASN cc_start: 0.8364 (t0) cc_final: 0.7743 (p0) outliers start: 152 outliers final: 113 residues processed: 544 average time/residue: 0.1985 time to fit residues: 182.5958 Evaluate side-chains 543 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 411 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 288 ARG Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 504 THR Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 789 GLU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 170 GLN Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 63 TRP Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 140 PHE Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 116 optimal weight: 0.0370 chunk 418 optimal weight: 20.0000 chunk 371 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 148 optimal weight: 0.0870 chunk 82 optimal weight: 7.9990 chunk 401 optimal weight: 20.0000 chunk 139 optimal weight: 0.9990 chunk 334 optimal weight: 2.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 218 ASN G 574 HIS H 208 HIS ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 442 GLN ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.071194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.062920 restraints weight = 109275.820| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.13 r_work: 0.3231 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.253 38233 Z= 0.387 Angle : 2.518 50.728 51994 Z= 1.439 Chirality : 0.438 6.386 5824 Planarity : 0.004 0.066 6532 Dihedral : 5.507 172.901 5234 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.65 % Allowed : 23.53 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.12), residues: 4710 helix: 1.51 (0.10), residues: 2657 sheet: -0.31 (0.30), residues: 333 loop : -0.46 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 16 TYR 0.027 0.001 TYR I 33 PHE 0.042 0.001 PHE N 140 TRP 0.020 0.001 TRP M 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01138 / 0.39 (38197) covalent geometry : angle 2.19021 / 1.44 (51901) hydrogen bonds : bond 0.04339 / 2.91 ( 1712) hydrogen bonds : angle 4.13471 / 2.95 ( 5136) metal coordination : bond 0.02038 / 1.40 ( 36) metal coordination : angle 29.43914 / 21.12 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 454 time to evaluate : 1.414 Fit side-chains revert: symmetry clash REVERT: F 36 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8548 (tp30) REVERT: F 182 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: F 358 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7818 (ttp-110) REVERT: G 70 MET cc_start: 0.9209 (mmm) cc_final: 0.8756 (mmm) REVERT: G 119 MET cc_start: 0.8881 (mmt) cc_final: 0.8632 (mmp) REVERT: G 150 MET cc_start: 0.8971 (tpt) cc_final: 0.8704 (tpp) REVERT: G 223 MET cc_start: 0.9120 (mmm) cc_final: 0.8866 (mmt) REVERT: G 292 PHE cc_start: 0.8617 (m-80) cc_final: 0.8345 (m-10) REVERT: G 509 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8694 (mm) REVERT: G 631 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8375 (ttp-110) REVERT: C 285 MET cc_start: 0.9155 (tpp) cc_final: 0.8628 (ttm) REVERT: C 571 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8374 (tp40) REVERT: B 16 ARG cc_start: 0.5639 (tpt170) cc_final: 0.4438 (tpm170) REVERT: B 22 GLN cc_start: 0.7900 (mp10) cc_final: 0.7535 (mp10) REVERT: B 193 TYR cc_start: 0.8024 (m-10) cc_final: 0.7733 (m-10) REVERT: I 13 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8804 (mp10) REVERT: I 27 LYS cc_start: 0.7952 (tppt) cc_final: 0.7598 (tppt) REVERT: H 118 PHE cc_start: 0.7786 (t80) cc_final: 0.7308 (t80) REVERT: H 122 MET cc_start: 0.8544 (mmp) cc_final: 0.8214 (mmm) REVERT: H 238 PHE cc_start: 0.7294 (p90) cc_final: 0.6653 (p90) REVERT: H 281 MET cc_start: 0.9077 (mmm) cc_final: 0.8787 (mmm) REVERT: H 284 LEU cc_start: 0.9086 (tp) cc_final: 0.8878 (mt) REVERT: A 30 MET cc_start: 0.8079 (ptm) cc_final: 0.7771 (tmm) REVERT: A 73 MET cc_start: 0.9159 (tmm) cc_final: 0.8734 (tmm) REVERT: A 74 PHE cc_start: 0.8964 (m-10) cc_final: 0.8632 (m-10) REVERT: L 168 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6110 (ttp) REVERT: L 377 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7398 (tt) REVERT: L 568 MET cc_start: 0.7412 (mmp) cc_final: 0.7106 (mmm) REVERT: L 598 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8566 (ttp) REVERT: M 63 TRP cc_start: 0.7827 (OUTLIER) cc_final: 0.6720 (m100) REVERT: M 121 MET cc_start: 0.7811 (mpp) cc_final: 0.7056 (mpp) REVERT: M 174 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8434 (t80) REVERT: M 364 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8434 (tm-30) REVERT: M 395 THR cc_start: 0.8734 (t) cc_final: 0.8358 (t) REVERT: M 442 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7635 (mpt180) REVERT: N 321 MET cc_start: 0.6913 (ptp) cc_final: 0.6603 (ptp) REVERT: K 31 MET cc_start: 0.8861 (ttm) cc_final: 0.8657 (ttm) REVERT: K 46 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7929 (t80) REVERT: J 73 MET cc_start: 0.8380 (mmm) cc_final: 0.8041 (mmm) REVERT: J 84 GLU cc_start: 0.7996 (pm20) cc_final: 0.7781 (pm20) REVERT: J 94 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8225 (mm) REVERT: J 98 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8154 (pt) REVERT: J 115 ASN cc_start: 0.8365 (t0) cc_final: 0.7766 (p0) outliers start: 103 outliers final: 72 residues processed: 536 average time/residue: 0.1974 time to fit residues: 178.0673 Evaluate side-chains 512 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 424 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 357 CYS Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 63 TRP Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 442 ARG Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 341 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 352 optimal weight: 20.0000 chunk 301 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 335 optimal weight: 6.9990 chunk 342 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 218 ASN I 23 HIS H 208 HIS ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 ASN L 442 GLN ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.069000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.060757 restraints weight = 109993.580| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.12 r_work: 0.3176 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 38233 Z= 0.411 Angle : 2.537 50.785 51994 Z= 1.447 Chirality : 0.439 6.400 5824 Planarity : 0.004 0.059 6532 Dihedral : 5.636 172.587 5234 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.63 % Allowed : 23.71 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.12), residues: 4710 helix: 1.42 (0.10), residues: 2658 sheet: -0.40 (0.30), residues: 333 loop : -0.47 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 40 TYR 0.035 0.002 TYR C 271 PHE 0.038 0.002 PHE N 140 TRP 0.015 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01172 / 0.41 (38197) covalent geometry : angle 2.20942 / 1.44 (51901) hydrogen bonds : bond 0.04908 / 3.30 ( 1712) hydrogen bonds : angle 4.28730 / 3.06 ( 5136) metal coordination : bond 0.02228 / 1.54 ( 36) metal coordination : angle 29.58632 / 21.26 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 416 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 36 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8473 (tp30) REVERT: F 182 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8332 (tm-30) REVERT: F 358 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8012 (ttp-110) REVERT: G 70 MET cc_start: 0.9222 (mmm) cc_final: 0.8799 (mmm) REVERT: G 119 MET cc_start: 0.9008 (mmp) cc_final: 0.8793 (mmp) REVERT: G 292 PHE cc_start: 0.8638 (m-80) cc_final: 0.8350 (m-10) REVERT: G 509 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8707 (mm) REVERT: G 631 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.8454 (ttp-110) REVERT: C 285 MET cc_start: 0.9160 (tpp) cc_final: 0.8698 (ttm) REVERT: C 571 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8463 (tp-100) REVERT: B 22 GLN cc_start: 0.7924 (mp10) cc_final: 0.7555 (mp10) REVERT: B 193 TYR cc_start: 0.7872 (m-10) cc_final: 0.7645 (m-10) REVERT: I 13 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8792 (mp10) REVERT: I 27 LYS cc_start: 0.7976 (tppt) cc_final: 0.7661 (tppt) REVERT: H 118 PHE cc_start: 0.8034 (t80) cc_final: 0.7537 (t80) REVERT: H 122 MET cc_start: 0.8686 (mmp) cc_final: 0.8389 (mmm) REVERT: H 238 PHE cc_start: 0.7406 (p90) cc_final: 0.6688 (p90) REVERT: H 284 LEU cc_start: 0.9114 (tp) cc_final: 0.8862 (mt) REVERT: A 73 MET cc_start: 0.9226 (tmm) cc_final: 0.8971 (tmm) REVERT: L 377 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7312 (tt) REVERT: L 568 MET cc_start: 0.7571 (mmp) cc_final: 0.7289 (mmm) REVERT: L 598 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8526 (ttp) REVERT: L 610 MET cc_start: 0.7851 (mmm) cc_final: 0.7595 (mmm) REVERT: M 63 TRP cc_start: 0.7837 (OUTLIER) cc_final: 0.6741 (m100) REVERT: M 121 MET cc_start: 0.8003 (mpp) cc_final: 0.7170 (mpp) REVERT: M 174 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8571 (t80) REVERT: M 364 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8392 (tm-30) REVERT: M 409 MET cc_start: 0.8146 (mtp) cc_final: 0.7894 (mtm) REVERT: M 460 MET cc_start: 0.7499 (mtm) cc_final: 0.7141 (ptp) REVERT: K 46 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.7962 (t80) REVERT: J 73 MET cc_start: 0.8435 (mmm) cc_final: 0.8017 (mmm) REVERT: J 94 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8275 (mm) REVERT: J 98 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8256 (pt) REVERT: J 115 ASN cc_start: 0.8353 (t0) cc_final: 0.7823 (p0) outliers start: 102 outliers final: 80 residues processed: 498 average time/residue: 0.1912 time to fit residues: 160.9030 Evaluate side-chains 506 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 412 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 276 THR Chi-restraints excluded: chain L residue 364 LYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 63 TRP Chi-restraints excluded: chain M residue 138 LEU Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 240 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 454 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 304 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 156 optimal weight: 4.9990 chunk 464 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 363 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 414 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 328 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 218 ASN H 208 HIS ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** M 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.070408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062160 restraints weight = 109457.946| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.12 r_work: 0.3211 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.249 38233 Z= 0.390 Angle : 2.525 50.762 51994 Z= 1.442 Chirality : 0.439 6.395 5824 Planarity : 0.004 0.061 6532 Dihedral : 5.558 172.932 5234 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.60 % Allowed : 23.94 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.13), residues: 4710 helix: 1.49 (0.10), residues: 2656 sheet: -0.25 (0.30), residues: 320 loop : -0.47 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 40 TYR 0.029 0.001 TYR C 271 PHE 0.046 0.001 PHE N 140 TRP 0.018 0.001 TRP M 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01140 / 0.39 (38197) covalent geometry : angle 2.19762 / 1.44 (51901) hydrogen bonds : bond 0.04531 / 3.04 ( 1712) hydrogen bonds : angle 4.19096 / 2.99 ( 5136) metal coordination : bond 0.01969 / 1.36 ( 36) metal coordination : angle 29.48869 / 21.15 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9334.39 seconds wall clock time: 160 minutes 26.22 seconds (9626.22 seconds total)