Starting phenix.real_space_refine on Sat Mar 7 01:59:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zci_14632/03_2026/7zci_14632.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zci_14632/03_2026/7zci_14632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zci_14632/03_2026/7zci_14632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zci_14632/03_2026/7zci_14632.map" model { file = "/net/cci-nas-00/data/ceres_data/7zci_14632/03_2026/7zci_14632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zci_14632/03_2026/7zci_14632.cif" } resolution = 2.69 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= 0.004 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 14 5.49 5 S 264 5.16 5 C 24104 2.51 5 N 6077 2.21 5 O 6489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36981 Number of models: 1 Model: "" Number of chains: 24 Chain: "F" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3432 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 416} 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: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4628 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 541} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1339 Classifications: {'peptide': 169} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 157} Chain breaks: 2 Chain: "I" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 12, 'TRANS': 132} Chain: "H" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2422 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 796 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 4593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4593 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 582} 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: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3635 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" 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: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 326 Unusual residues: {'3PE': 6, 'LFA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'3PE': 1, 'LFA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" 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 2746 SG CYS F 354 68.150 57.318 195.911 1.00 10.27 S ATOM 2766 SG CYS F 357 71.442 56.678 200.357 1.00 28.74 S ATOM 3087 SG CYS F 398 65.720 53.108 200.507 1.00 16.21 S ATOM 2722 SG CYS F 351 70.348 50.925 197.071 1.00 13.11 S ATOM 4079 SG CYS E 92 78.163 48.304 216.984 1.00 34.08 S ATOM 4113 SG CYS E 97 78.233 48.890 220.480 1.00 28.08 S ATOM 4391 SG CYS E 133 72.994 47.699 216.395 1.00 39.84 S ATOM 4417 SG CYS E 137 72.080 48.369 219.596 1.00 34.04 S ATOM 5501 SG CYS G 114 79.175 64.493 179.115 1.00 12.54 S ATOM 5441 SG CYS G 105 84.223 68.327 181.081 1.00 10.85 S ATOM 5461 SG CYS G 108 85.122 62.433 178.530 1.00 10.85 S ATOM 5855 SG CYS G 156 73.417 56.229 183.449 1.00 11.35 S ATOM 5836 SG CYS G 153 79.183 55.135 186.711 1.00 9.34 S ATOM 5884 SG CYS G 159 76.508 50.695 182.942 1.00 3.40 S ATOM 6232 SG CYS G 203 78.663 56.029 180.052 1.00 37.43 S ATOM 6457 SG CYS G 230 76.320 48.609 158.592 1.00 7.69 S ATOM 6742 SG CYS G 265 76.269 44.520 163.680 1.00 15.85 S ATOM 6505 SG CYS G 237 70.853 47.894 161.436 1.00 11.69 S ATOM 6481 SG CYS G 233 73.361 42.819 158.279 1.00 13.60 S ATOM 4902 SG CYS G 36 66.794 57.049 186.141 1.00 6.75 S ATOM 4978 SG CYS G 47 68.356 60.420 186.687 1.00 2.58 S ATOM 5004 SG CYS G 50 62.540 61.902 186.238 1.00 18.72 S ATOM 5153 SG CYS G 69 62.093 58.302 185.841 1.00 13.40 S ATOM 16924 SG CYS B 129 89.755 92.902 156.854 1.00 27.53 S ATOM 16560 SG CYS B 64 94.806 96.700 158.804 1.00 73.84 S ATOM 16554 SG CYS B 63 88.948 98.393 160.527 1.00 66.08 S ATOM 17141 SG CYS B 158 91.451 92.655 162.716 1.00 41.03 S ATOM 18185 SG CYS I 102 90.041 86.409 168.533 1.00 11.20 S ATOM 18160 SG CYS I 99 95.569 85.362 164.963 1.00 6.69 S ATOM 18203 SG CYS I 105 93.988 81.776 170.260 1.00 13.57 S ATOM 17918 SG CYS I 70 90.357 81.340 164.828 1.00 11.64 S ATOM 18232 SG CYS I 109 94.908 76.131 176.203 1.00 12.85 S ATOM 17895 SG CYS I 66 93.129 75.580 170.026 1.00 11.15 S ATOM 17855 SG CYS I 60 97.251 71.285 172.263 1.00 8.14 S ATOM 17873 SG CYS I 63 90.917 71.612 174.669 1.00 8.05 S Time building chain proxies: 7.94, per 1000 atoms: 0.21 Number of scatterers: 36981 At special positions: 0 Unit cell: (156.88, 209.88, 249.1, 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 264 16.00 P 14 15.00 O 6489 8.00 N 6077 7.00 C 24104 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: 3.25 Conformation dependent library (CDL) restraints added in 1.6 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="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " 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="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " 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="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " 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="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " Number of angles added : 93 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8492 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 0 sheets defined 53.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 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 107 Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 137 through 153 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 238 Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.902A pdb=" N ASP F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 302 through 306' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 349 Processing helix chain 'F' and resid 355 through 373 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 422 Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.569A pdb=" N SER E 36 " --> pdb=" O PRO E 32 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.141A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 99 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: 4.729A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.589A 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 276 removed outlier: 4.866A pdb=" N TYR G 272 " --> pdb=" O GLY G 268 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY G 273 " --> pdb=" O ARG G 269 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR G 274 " --> pdb=" O PHE G 270 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN G 276 " --> pdb=" O TYR G 272 " (cutoff:3.500A) 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 368 through 373 removed outlier: 4.280A pdb=" N GLU G 372 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER G 373 " --> pdb=" O ARG G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' 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: 4.562A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 424 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 601 through 605 removed outlier: 4.683A pdb=" N ASN G 605 " --> pdb=" O ALA G 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 605' Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 690 removed outlier: 5.274A pdb=" N GLY G 687 " --> pdb=" O PRO G 683 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE G 688 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS G 689 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASP G 690 " --> pdb=" O ALA G 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 683 through 690' Processing helix chain 'G' and resid 764 through 768 removed outlier: 5.052A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 768' Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 833 through 836 No H-bonds generated for 'chain 'G' and resid 833 through 836' 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 65 removed outlier: 5.016A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 removed outlier: 4.973A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 326 Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 427 through 432 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 570 Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 No H-bonds generated for 'chain 'I' and resid 127 through 130' Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' Processing helix chain 'H' and resid 6 through 39 Processing helix chain 'H' and resid 56 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 5.138A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 137 removed outlier: 4.660A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.036A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 231 through 257 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 322 removed outlier: 4.879A pdb=" N LEU H 306 " --> pdb=" O TRP H 302 " (cutoff:3.500A) Proline residue: H 307 - end of helix Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 89 Processing helix chain 'A' and resid 97 through 120 Processing helix chain 'L' and resid 4 through 20 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 131 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: 4.310A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N MET L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 256 Processing helix chain 'L' and resid 261 through 268 Processing helix chain 'L' and resid 270 through 273 No H-bonds generated for 'chain 'L' and resid 270 through 273' Processing helix chain 'L' and resid 277 through 298 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 355 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 436 Processing helix chain 'L' and resid 455 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 511 Processing helix chain 'L' and resid 517 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 560 removed outlier: 4.964A pdb=" N LYS L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) Proline residue: L 552 - end of helix 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 49 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 145 Processing helix chain 'M' and resid 147 through 156 Processing helix chain 'M' and resid 165 through 199 Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 217 through 233 Processing helix chain 'M' and resid 243 through 249 Processing helix chain 'M' and resid 256 through 262 Processing helix chain 'M' and resid 266 through 275 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 396 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 501 removed outlier: 4.887A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) 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 57 Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix Processing helix chain 'N' and resid 103 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 180 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: 4.410A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 288 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 320 through 347 removed outlier: 5.195A pdb=" N GLU N 324 " --> pdb=" O GLU N 320 " (cutoff:3.500A) 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: 4.369A 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 479 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 57 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 111 removed outlier: 5.280A 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 1685 hydrogen bonds defined for protein. 5055 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: 5.96 Time building geometry restraints manager: 4.26 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: 15662 1.42 - 1.64: 21734 1.64 - 1.86: 403 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 37891 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.382 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.602 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.372 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C10 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.443 1.379 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O13 3PE L 803 " pdb=" P 3PE L 803 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.15e+00 ... (remaining 37886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 50606 2.85 - 5.70: 611 5.70 - 8.55: 113 8.55 - 11.40: 14 11.40 - 14.25: 7 Bond angle restraints: 51351 Sorted by residual: angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 96.89 12.92 2.21e+00 2.05e-01 3.42e+01 angle pdb=" N GLU C 202 " pdb=" CA GLU C 202 " pdb=" C GLU C 202 " ideal model delta sigma weight residual 114.31 107.24 7.07 1.29e+00 6.01e-01 3.00e+01 angle pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta sigma weight residual 121.80 133.46 -11.66 2.44e+00 1.68e-01 2.28e+01 angle pdb=" C ALA G 177 " pdb=" N HIS G 178 " pdb=" CA HIS G 178 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" CB MET L 243 " pdb=" CG MET L 243 " pdb=" SD MET L 243 " ideal model delta sigma weight residual 112.70 126.56 -13.86 3.00e+00 1.11e-01 2.13e+01 ... (remaining 51346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.36: 20637 23.36 - 46.72: 1457 46.72 - 70.09: 262 70.09 - 93.45: 46 93.45 - 116.81: 6 Dihedral angle restraints: 22408 sinusoidal: 9132 harmonic: 13276 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 180.00 135.87 44.13 0 5.00e+00 4.00e-02 7.79e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.81 34.19 0 5.00e+00 4.00e-02 4.67e+01 dihedral pdb=" CA ILE E 145 " pdb=" C ILE E 145 " pdb=" N ASP E 146 " pdb=" CA ASP E 146 " ideal model delta harmonic sigma weight residual -180.00 -146.20 -33.80 0 5.00e+00 4.00e-02 4.57e+01 ... (remaining 22405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.240: 5690 4.240 - 8.480: 0 8.480 - 12.720: 0 12.720 - 16.959: 0 16.959 - 21.199: 28 Chirality restraints: 5718 Sorted by residual: chirality pdb="FE1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " pdb=" S4 SF4 G1002 " both_signs ideal model delta sigma weight residual False -10.55 10.64 -21.20 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.63 21.18 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 -10.62 21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5715 not shown) Planarity restraints: 6398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 89 " 0.065 5.00e-02 4.00e+02 9.86e-02 1.56e+01 pdb=" N PRO J 90 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO J 90 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO J 90 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 174 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" CD GLU B 174 " -0.057 2.00e-02 2.50e+03 pdb=" OE1 GLU B 174 " 0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU B 174 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C VAL N 63 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.021 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.019 2.00e-02 2.50e+03 ... (remaining 6395 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 5089 2.75 - 3.29: 35621 3.29 - 3.83: 68074 3.83 - 4.36: 82665 4.36 - 4.90: 137674 Nonbonded interactions: 329123 Sorted by model distance: nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.217 3.040 nonbonded pdb=" OE2 GLU N 324 " pdb=" OH TYR N 397 " model vdw 2.233 3.040 nonbonded pdb=" O LEU C 429 " pdb=" OG1 THR C 432 " model vdw 2.238 3.040 nonbonded pdb=" OG SER L 37 " pdb=" OD1 ASN L 121 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASP L 563 " pdb=" OH TYR M 300 " model vdw 2.241 3.040 ... (remaining 329118 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 36.470 Find NCS groups from input model: 0.240 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:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 : 0.007 0.168 37927 Z= 0.292 Angle : 0.856 14.247 51444 Z= 0.429 Chirality : 1.478 21.199 5718 Planarity : 0.007 0.099 6398 Dihedral : 16.216 116.811 13916 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 1.77 % Allowed : 16.26 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.11), residues: 4606 helix: 0.21 (0.09), residues: 2689 sheet: -0.63 (0.28), residues: 305 loop : -0.71 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 287 TYR 0.044 0.003 TYR M 197 PHE 0.035 0.003 PHE L 341 TRP 0.037 0.002 TRP N 53 HIS 0.009 0.001 HIS M 322 Details of bonding type rmsd covalent geometry : bond 0.00670 (37891) covalent geometry : angle 0.83688 (51351) hydrogen bonds : bond 0.06789 ( 1685) hydrogen bonds : angle 4.94750 ( 5055) metal coordination : bond 0.05465 ( 36) metal coordination : angle 4.34458 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 522 time to evaluate : 1.394 Fit side-chains REVERT: F 243 LYS cc_start: 0.9037 (mtmt) cc_final: 0.8592 (mptt) REVERT: E 163 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8899 (mm-30) REVERT: G 310 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7867 (mp10) REVERT: G 345 HIS cc_start: 0.9101 (t-90) cc_final: 0.8724 (t-90) REVERT: G 851 LYS cc_start: 0.9141 (ttmm) cc_final: 0.8827 (tttt) REVERT: C 200 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8352 (mtpp) REVERT: C 377 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: C 405 LYS cc_start: 0.7565 (ttmm) cc_final: 0.6793 (ttmm) REVERT: C 409 GLN cc_start: 0.8123 (mt0) cc_final: 0.7293 (mt0) REVERT: C 482 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8595 (tm-30) REVERT: B 39 MET cc_start: 0.5647 (pmt) cc_final: 0.5387 (pmm) REVERT: H 260 TRP cc_start: 0.9016 (p-90) cc_final: 0.8677 (p90) REVERT: A 30 MET cc_start: 0.8674 (ttm) cc_final: 0.8341 (ttm) REVERT: M 109 ILE cc_start: 0.7925 (pt) cc_final: 0.7723 (pp) REVERT: M 466 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7781 (t80) REVERT: N 30 TRP cc_start: 0.8497 (t60) cc_final: 0.8191 (t-100) REVERT: N 321 MET cc_start: 0.8487 (ptp) cc_final: 0.8282 (ptm) REVERT: J 88 LEU cc_start: 0.8090 (mt) cc_final: 0.7808 (mt) outliers start: 67 outliers final: 40 residues processed: 574 average time/residue: 0.7995 time to fit residues: 546.7330 Evaluate side-chains 551 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 509 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 660 THR Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 466 PHE Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 224 ASN F 409 GLN G 54 GLN G 238 ASN G 728 GLN C 359 HIS B 52 ASN B 196 ASN M 19 GLN M 119 ASN M 502 ASN N 449 GLN K 5 GLN K 82 GLN J 24 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.070202 restraints weight = 40524.324| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.04 r_work: 0.2809 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.253 37927 Z= 0.409 Angle : 2.507 50.524 51444 Z= 1.443 Chirality : 0.452 6.648 5718 Planarity : 0.005 0.063 6398 Dihedral : 9.802 116.424 5774 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.28 % Favored : 97.70 % Rotamer: Outliers : 3.01 % Allowed : 14.12 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: 0.43 (0.12), residues: 4606 helix: 0.94 (0.10), residues: 2685 sheet: -0.59 (0.28), residues: 298 loop : -0.51 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 287 TYR 0.026 0.002 TYR H 242 PHE 0.028 0.002 PHE L 341 TRP 0.024 0.001 TRP L 143 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01168 (37891) covalent geometry : angle 2.19136 (51351) hydrogen bonds : bond 0.05626 ( 1685) hydrogen bonds : angle 4.43651 ( 5055) metal coordination : bond 0.05487 ( 36) metal coordination : angle 28.73562 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 534 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 114 ASN cc_start: 0.8712 (m-40) cc_final: 0.8494 (t0) REVERT: G 85 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: G 345 HIS cc_start: 0.8985 (t-90) cc_final: 0.8639 (t-90) REVERT: C 200 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8724 (mtpp) REVERT: C 377 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: C 405 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8243 (ttmm) REVERT: B 202 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: B 207 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: H 13 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8204 (tt) REVERT: H 260 TRP cc_start: 0.8889 (p-90) cc_final: 0.8641 (p90) REVERT: L 407 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8068 (tmm) REVERT: M 26 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6495 (pptt) REVERT: M 109 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8246 (pp) REVERT: N 30 TRP cc_start: 0.8224 (t60) cc_final: 0.7763 (t-100) REVERT: N 31 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7767 (ttp-110) REVERT: N 200 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: N 388 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8046 (mpp) REVERT: K 46 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.7930 (t80) REVERT: K 88 GLN cc_start: 0.8246 (mp10) cc_final: 0.8041 (mm-40) outliers start: 114 outliers final: 49 residues processed: 599 average time/residue: 0.7602 time to fit residues: 543.8245 Evaluate side-chains 570 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 509 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain M residue 26 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 403 optimal weight: 9.9990 chunk 423 optimal weight: 0.9990 chunk 395 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 314 optimal weight: 10.0000 chunk 336 optimal weight: 0.0770 chunk 42 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN F 431 HIS G 238 ASN G 583 ASN G 728 GLN C 228 HIS B 52 ASN B 196 ASN H 226 HIS M 119 ASN M 322 HIS M 502 ASN N 449 GLN K 5 GLN K 82 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.091204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.070569 restraints weight = 40104.809| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.04 r_work: 0.2819 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.249 37927 Z= 0.399 Angle : 2.506 50.623 51444 Z= 1.443 Chirality : 0.449 6.572 5718 Planarity : 0.004 0.060 6398 Dihedral : 9.421 112.882 5743 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.43 % Favored : 97.55 % Rotamer: Outliers : 2.90 % Allowed : 14.81 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: 0.77 (0.12), residues: 4606 helix: 1.22 (0.10), residues: 2696 sheet: -0.46 (0.28), residues: 308 loop : -0.38 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 287 TYR 0.025 0.002 TYR H 242 PHE 0.027 0.002 PHE L 341 TRP 0.024 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01150 (37891) covalent geometry : angle 2.18796 (51351) hydrogen bonds : bond 0.05302 ( 1685) hydrogen bonds : angle 4.30979 ( 5055) metal coordination : bond 0.04648 ( 36) metal coordination : angle 28.80738 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 531 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 85 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8017 (tt0) REVERT: G 187 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: G 345 HIS cc_start: 0.9023 (t-90) cc_final: 0.8655 (t-90) REVERT: C 127 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.8363 (t80) REVERT: C 328 GLN cc_start: 0.8058 (mt0) cc_final: 0.7773 (mt0) REVERT: C 358 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8665 (ttt) REVERT: C 482 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: B 207 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: H 13 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8220 (tt) REVERT: H 209 ARG cc_start: 0.8370 (mmm160) cc_final: 0.8145 (mmm160) REVERT: H 260 TRP cc_start: 0.8897 (p-90) cc_final: 0.8603 (p90) REVERT: A 30 MET cc_start: 0.8576 (ttm) cc_final: 0.8148 (ptm) REVERT: L 185 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8359 (mp) REVERT: L 407 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8126 (tmm) REVERT: M 109 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8227 (pp) REVERT: N 30 TRP cc_start: 0.8177 (t60) cc_final: 0.7765 (t-100) REVERT: N 154 GLU cc_start: 0.8121 (tt0) cc_final: 0.7818 (tt0) REVERT: N 200 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: N 388 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8058 (mpp) REVERT: K 46 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.7921 (t80) REVERT: K 88 GLN cc_start: 0.8235 (mp10) cc_final: 0.8028 (mm-40) REVERT: K 97 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7691 (pm20) REVERT: K 98 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8215 (mtp) REVERT: J 1 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7350 (ttm) outliers start: 110 outliers final: 52 residues processed: 596 average time/residue: 0.7993 time to fit residues: 566.0998 Evaluate side-chains 577 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 510 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 146 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 299 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 359 optimal weight: 10.0000 chunk 380 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 325 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN G 54 GLN G 56 GLN G 238 ASN G 728 GLN C 154 ASN B 52 ASN B 196 ASN L 315 GLN M 117 HIS M 119 ASN M 322 HIS M 335 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 502 ASN N 449 GLN K 5 GLN K 82 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.069322 restraints weight = 39724.890| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.03 r_work: 0.2792 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.251 37927 Z= 0.418 Angle : 2.513 50.716 51444 Z= 1.446 Chirality : 0.451 6.633 5718 Planarity : 0.005 0.062 6398 Dihedral : 9.448 110.946 5736 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer: Outliers : 3.54 % Allowed : 14.92 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.82 (0.12), residues: 4606 helix: 1.26 (0.10), residues: 2701 sheet: -0.42 (0.28), residues: 306 loop : -0.39 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 31 TYR 0.025 0.002 TYR H 242 PHE 0.027 0.002 PHE L 341 TRP 0.027 0.002 TRP L 143 HIS 0.012 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01183 (37891) covalent geometry : angle 2.19747 (51351) hydrogen bonds : bond 0.05825 ( 1685) hydrogen bonds : angle 4.36608 ( 5055) metal coordination : bond 0.05265 ( 36) metal coordination : angle 28.74069 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 533 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: F 335 MET cc_start: 0.9157 (mmm) cc_final: 0.8932 (mmp) REVERT: G 85 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: G 298 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: G 345 HIS cc_start: 0.9047 (t-90) cc_final: 0.8672 (t-90) REVERT: G 773 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: G 834 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8172 (mm-40) REVERT: C 127 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.8503 (t80) REVERT: C 328 GLN cc_start: 0.8108 (mt0) cc_final: 0.7817 (mt0) REVERT: C 358 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8666 (ttt) REVERT: C 482 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: C 600 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.5737 (ptp90) REVERT: B 170 MET cc_start: 0.7867 (mmt) cc_final: 0.7660 (mmt) REVERT: B 202 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: H 13 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8239 (tt) REVERT: H 260 TRP cc_start: 0.8909 (p-90) cc_final: 0.8594 (p90) REVERT: A 30 MET cc_start: 0.8660 (ttm) cc_final: 0.8153 (ptm) REVERT: L 407 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8187 (tmm) REVERT: L 581 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8231 (mptt) REVERT: M 109 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8283 (pp) REVERT: M 304 MET cc_start: 0.9126 (mmm) cc_final: 0.8923 (mmm) REVERT: M 335 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8232 (tp40) REVERT: M 373 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7483 (mpm) REVERT: N 200 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: N 388 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8001 (mpp) REVERT: K 88 GLN cc_start: 0.8270 (mp10) cc_final: 0.8032 (mm-40) REVERT: K 97 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7731 (pm20) REVERT: K 98 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8191 (mtp) REVERT: J 24 ASN cc_start: 0.8785 (t0) cc_final: 0.8577 (t0) REVERT: J 59 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8428 (t80) outliers start: 134 outliers final: 59 residues processed: 613 average time/residue: 0.7979 time to fit residues: 582.4164 Evaluate side-chains 600 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 522 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 335 GLN Chi-restraints excluded: chain M residue 373 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 249 optimal weight: 5.9990 chunk 333 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 311 optimal weight: 0.4980 chunk 314 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 106 optimal weight: 0.0980 chunk 194 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 409 GLN G 238 ASN G 728 GLN C 154 ASN B 52 ASN B 196 ASN A 13 HIS M 119 ASN M 322 HIS ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 502 ASN N 7 ASN N 449 GLN K 5 GLN K 82 GLN J 86 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.090603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.069985 restraints weight = 39563.567| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.04 r_work: 0.2808 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.250 37927 Z= 0.402 Angle : 2.508 50.659 51444 Z= 1.444 Chirality : 0.449 6.567 5718 Planarity : 0.004 0.063 6398 Dihedral : 9.331 112.521 5736 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.52 % Favored : 97.46 % Rotamer: Outliers : 3.38 % Allowed : 15.39 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.12), residues: 4606 helix: 1.38 (0.10), residues: 2699 sheet: -0.39 (0.28), residues: 308 loop : -0.35 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 85 TYR 0.026 0.002 TYR H 242 PHE 0.028 0.002 PHE C 340 TRP 0.026 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01156 (37891) covalent geometry : angle 2.19078 (51351) hydrogen bonds : bond 0.05435 ( 1685) hydrogen bonds : angle 4.30179 ( 5055) metal coordination : bond 0.04406 ( 36) metal coordination : angle 28.82019 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 531 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: F 335 MET cc_start: 0.9155 (mmm) cc_final: 0.8934 (mmp) REVERT: G 85 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: G 345 HIS cc_start: 0.9061 (t-90) cc_final: 0.8685 (t-90) REVERT: G 773 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: G 808 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8379 (pt0) REVERT: G 834 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8179 (mm-40) REVERT: C 127 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8391 (t80) REVERT: C 200 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8807 (mtpp) REVERT: C 328 GLN cc_start: 0.8092 (mt0) cc_final: 0.7799 (mt0) REVERT: C 358 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8676 (ttt) REVERT: C 391 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8360 (tp) REVERT: C 482 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: C 600 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.5739 (ptp90) REVERT: B 174 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: B 197 MET cc_start: 0.8528 (mtp) cc_final: 0.8328 (mmm) REVERT: B 202 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: H 13 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8227 (tt) REVERT: A 30 MET cc_start: 0.8561 (ttm) cc_final: 0.8090 (ptm) REVERT: L 185 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8360 (mp) REVERT: L 407 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8141 (tmm) REVERT: L 490 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7600 (ttp) REVERT: L 529 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7483 (mtt-85) REVERT: L 581 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8209 (mptt) REVERT: M 109 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8261 (pp) REVERT: M 373 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7528 (mpm) REVERT: N 200 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: K 88 GLN cc_start: 0.8266 (mp10) cc_final: 0.8030 (mm-40) REVERT: K 97 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7722 (pm20) REVERT: K 98 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8089 (mtp) REVERT: J 24 ASN cc_start: 0.8778 (t0) cc_final: 0.8528 (t0) REVERT: J 59 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8468 (t80) outliers start: 128 outliers final: 62 residues processed: 610 average time/residue: 0.7698 time to fit residues: 560.4318 Evaluate side-chains 602 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 518 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 238 ASN Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain L residue 529 ARG Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 373 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 388 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 356 optimal weight: 4.9990 chunk 258 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 408 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 395 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN G 56 GLN G 238 ASN G 728 GLN C 544 ASN B 52 ASN B 196 ASN M 119 ASN M 322 HIS M 335 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 GLN K 5 GLN K 82 GLN J 86 GLN J 115 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.090402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.069834 restraints weight = 39722.293| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.03 r_work: 0.2802 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.250 37927 Z= 0.407 Angle : 2.510 50.683 51444 Z= 1.445 Chirality : 0.449 6.584 5718 Planarity : 0.004 0.063 6398 Dihedral : 9.161 112.226 5729 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer: Outliers : 3.70 % Allowed : 15.52 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 4606 helix: 1.39 (0.10), residues: 2699 sheet: -0.35 (0.28), residues: 306 loop : -0.34 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 85 TYR 0.029 0.002 TYR H 242 PHE 0.029 0.002 PHE C 340 TRP 0.026 0.001 TRP L 143 HIS 0.011 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01165 (37891) covalent geometry : angle 2.19386 (51351) hydrogen bonds : bond 0.05552 ( 1685) hydrogen bonds : angle 4.30721 ( 5055) metal coordination : bond 0.04614 ( 36) metal coordination : angle 28.78697 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 528 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: F 238 ASN cc_start: 0.8386 (m-40) cc_final: 0.8167 (m-40) REVERT: F 241 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8616 (tppp) REVERT: F 335 MET cc_start: 0.9148 (mmm) cc_final: 0.8937 (mmp) REVERT: G 85 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: G 187 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: G 773 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7541 (pt0) REVERT: G 808 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8364 (pt0) REVERT: G 834 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8180 (mm-40) REVERT: C 127 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.8436 (t80) REVERT: C 200 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8837 (mtpp) REVERT: C 328 GLN cc_start: 0.8089 (mt0) cc_final: 0.7786 (mt0) REVERT: C 358 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8671 (ttt) REVERT: C 391 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8386 (tp) REVERT: C 482 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: C 600 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.5738 (ptp90) REVERT: B 68 MET cc_start: 0.8133 (ptt) cc_final: 0.7776 (ttp) REVERT: B 170 MET cc_start: 0.8150 (mmt) cc_final: 0.7702 (mmt) REVERT: B 202 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: H 13 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8227 (tt) REVERT: A 30 MET cc_start: 0.8600 (ttm) cc_final: 0.8056 (ptm) REVERT: L 185 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8365 (mp) REVERT: L 407 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8141 (tmm) REVERT: L 529 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7493 (mtt-85) REVERT: L 581 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8211 (mptt) REVERT: M 107 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7250 (ptmt) REVERT: M 109 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8289 (pp) REVERT: M 335 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8230 (tp40) REVERT: M 373 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7550 (mpm) REVERT: N 200 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: K 88 GLN cc_start: 0.8290 (mp10) cc_final: 0.8061 (mm110) REVERT: K 98 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8098 (mtp) REVERT: J 24 ASN cc_start: 0.8806 (t0) cc_final: 0.8558 (t0) REVERT: J 59 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8474 (t80) outliers start: 140 outliers final: 66 residues processed: 612 average time/residue: 0.7794 time to fit residues: 570.8559 Evaluate side-chains 608 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 518 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain L residue 529 ARG Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 335 GLN Chi-restraints excluded: chain M residue 373 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 303 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 381 optimal weight: 20.0000 chunk 300 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 248 optimal weight: 0.5980 chunk 377 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN G 238 ASN G 728 GLN G 768 ASN B 52 ASN B 196 ASN M 119 ASN M 322 HIS ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 GLN K 5 GLN K 82 GLN J 86 GLN J 115 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.068908 restraints weight = 39534.547| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.02 r_work: 0.2782 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.251 37927 Z= 0.428 Angle : 2.518 50.726 51444 Z= 1.448 Chirality : 0.452 6.642 5718 Planarity : 0.005 0.062 6398 Dihedral : 9.356 112.164 5729 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer: Outliers : 3.46 % Allowed : 15.84 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.88 (0.12), residues: 4606 helix: 1.30 (0.10), residues: 2699 sheet: -0.31 (0.28), residues: 307 loop : -0.36 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 31 TYR 0.030 0.002 TYR H 242 PHE 0.031 0.002 PHE C 340 TRP 0.029 0.002 TRP L 143 HIS 0.012 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01202 (37891) covalent geometry : angle 2.20315 (51351) hydrogen bonds : bond 0.05994 ( 1685) hydrogen bonds : angle 4.38631 ( 5055) metal coordination : bond 0.05292 ( 36) metal coordination : angle 28.74179 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 521 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 241 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8641 (tppp) REVERT: G 85 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: G 187 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8200 (pm20) REVERT: G 298 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: G 773 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: G 834 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8184 (mm-40) REVERT: C 127 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.8500 (t80) REVERT: C 200 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8847 (mtpp) REVERT: C 328 GLN cc_start: 0.8156 (mt0) cc_final: 0.7861 (mt0) REVERT: C 358 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8678 (ttt) REVERT: C 391 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8396 (tp) REVERT: C 482 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: B 68 MET cc_start: 0.8178 (ptt) cc_final: 0.7829 (ttp) REVERT: B 174 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7881 (pm20) REVERT: B 202 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: H 13 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8236 (tt) REVERT: L 407 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8191 (tmm) REVERT: L 529 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7507 (mtt-85) REVERT: L 581 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8240 (mptt) REVERT: M 107 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7246 (ptmt) REVERT: M 109 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8322 (pp) REVERT: M 373 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7497 (mpm) REVERT: N 200 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: K 72 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: K 88 GLN cc_start: 0.8314 (mp10) cc_final: 0.8112 (mm-40) REVERT: K 98 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8117 (mtp) REVERT: J 18 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8387 (mtp180) REVERT: J 24 ASN cc_start: 0.8861 (t0) cc_final: 0.8593 (t0) REVERT: J 59 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.8521 (t80) outliers start: 131 outliers final: 69 residues processed: 599 average time/residue: 0.7971 time to fit residues: 569.0878 Evaluate side-chains 600 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 507 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain L residue 529 ARG Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 373 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 386 ILE Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 435 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 433 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 270 optimal weight: 9.9990 chunk 334 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN G 238 ASN G 283 GLN G 728 GLN B 52 ASN B 196 ASN M 119 ASN M 322 HIS M 335 GLN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 GLN K 5 GLN K 82 GLN J 86 GLN J 115 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.089334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.068965 restraints weight = 39312.767| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 0.99 r_work: 0.2785 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.251 37927 Z= 0.433 Angle : 2.521 50.725 51444 Z= 1.450 Chirality : 0.452 6.657 5718 Planarity : 0.005 0.059 6398 Dihedral : 9.520 113.054 5729 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 3.38 % Allowed : 16.13 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.81 (0.12), residues: 4606 helix: 1.24 (0.10), residues: 2700 sheet: -0.30 (0.29), residues: 307 loop : -0.39 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 31 TYR 0.030 0.002 TYR H 242 PHE 0.033 0.002 PHE C 340 TRP 0.029 0.002 TRP L 143 HIS 0.013 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01212 (37891) covalent geometry : angle 2.20767 (51351) hydrogen bonds : bond 0.06134 ( 1685) hydrogen bonds : angle 4.43475 ( 5055) metal coordination : bond 0.05362 ( 36) metal coordination : angle 28.73135 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 520 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: F 241 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8593 (tppp) REVERT: G 85 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: G 187 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: G 298 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: G 718 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8346 (ttt180) REVERT: G 773 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7505 (pt0) REVERT: G 834 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8142 (mm-40) REVERT: C 127 PHE cc_start: 0.9468 (OUTLIER) cc_final: 0.8474 (t80) REVERT: C 200 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8825 (mtpp) REVERT: C 358 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8668 (ttt) REVERT: C 391 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8390 (tp) REVERT: B 68 MET cc_start: 0.8157 (ptt) cc_final: 0.7836 (ttp) REVERT: B 202 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: H 13 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8255 (tt) REVERT: H 260 TRP cc_start: 0.8835 (p-90) cc_final: 0.8616 (p90) REVERT: L 407 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8213 (tmm) REVERT: L 581 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8322 (mptt) REVERT: M 109 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8346 (pp) REVERT: M 373 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7553 (mpm) REVERT: N 200 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: K 72 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7465 (pt0) REVERT: K 88 GLN cc_start: 0.8345 (mp10) cc_final: 0.8112 (mm110) REVERT: K 98 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8179 (mtp) REVERT: J 18 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8370 (mtp180) REVERT: J 24 ASN cc_start: 0.8872 (t0) cc_final: 0.8619 (t0) REVERT: J 59 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8605 (t80) outliers start: 128 outliers final: 65 residues processed: 598 average time/residue: 0.8002 time to fit residues: 567.2859 Evaluate side-chains 598 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 512 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 718 ARG Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 835 SER Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 102 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 407 MET Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 373 MET Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 386 ILE Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 325 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 447 optimal weight: 2.9990 chunk 284 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 337 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN G 56 GLN G 137 HIS G 238 ASN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 728 GLN B 52 ASN B 196 ASN M 119 ASN M 322 HIS ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 GLN K 5 GLN K 82 GLN J 86 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.071063 restraints weight = 39491.677| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.01 r_work: 0.2829 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.248 37927 Z= 0.394 Angle : 2.512 50.618 51444 Z= 1.444 Chirality : 0.447 6.514 5718 Planarity : 0.004 0.063 6398 Dihedral : 9.163 117.698 5728 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.56 % Allowed : 17.00 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.12), residues: 4606 helix: 1.50 (0.10), residues: 2694 sheet: -0.29 (0.29), residues: 308 loop : -0.31 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 31 TYR 0.031 0.002 TYR H 242 PHE 0.031 0.001 PHE C 340 TRP 0.025 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01142 (37891) covalent geometry : angle 2.19257 (51351) hydrogen bonds : bond 0.05162 ( 1685) hydrogen bonds : angle 4.26096 ( 5055) metal coordination : bond 0.03712 ( 36) metal coordination : angle 28.92139 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 525 time to evaluate : 1.209 Fit side-chains REVERT: F 241 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8558 (tppp) REVERT: F 335 MET cc_start: 0.9135 (mmm) cc_final: 0.8933 (mmp) REVERT: G 85 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: G 187 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: G 345 HIS cc_start: 0.9053 (t-90) cc_final: 0.8703 (t-90) REVERT: G 773 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7527 (pt0) REVERT: G 834 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8158 (mm-40) REVERT: C 127 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.8444 (t80) REVERT: C 328 GLN cc_start: 0.8106 (mt0) cc_final: 0.7729 (mt0) REVERT: C 391 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8381 (tp) REVERT: C 600 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.5714 (ptp90) REVERT: B 68 MET cc_start: 0.8164 (ptt) cc_final: 0.7868 (ttp) REVERT: B 146 ASP cc_start: 0.8908 (p0) cc_final: 0.8497 (p0) REVERT: B 170 MET cc_start: 0.8015 (mmt) cc_final: 0.7730 (mmt) REVERT: B 202 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: H 13 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8221 (tt) REVERT: A 30 MET cc_start: 0.8606 (ttm) cc_final: 0.8193 (ptm) REVERT: L 185 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8415 (mp) REVERT: L 581 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8242 (mptt) REVERT: M 109 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8310 (pp) REVERT: N 61 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7322 (pmm) REVERT: K 88 GLN cc_start: 0.8312 (mp10) cc_final: 0.8074 (mm-40) REVERT: K 97 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7785 (pm20) REVERT: K 98 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8022 (mtp) REVERT: J 24 ASN cc_start: 0.8805 (t0) cc_final: 0.8533 (t0) REVERT: J 59 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8526 (t80) outliers start: 97 outliers final: 46 residues processed: 580 average time/residue: 0.7884 time to fit residues: 544.8625 Evaluate side-chains 571 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 509 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 521 SER Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 386 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 41 optimal weight: 7.9990 chunk 362 optimal weight: 0.0020 chunk 304 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 283 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 379 optimal weight: 7.9990 chunk 430 optimal weight: 6.9990 chunk 63 optimal weight: 0.1980 chunk 303 optimal weight: 8.9990 overall best weight: 3.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 409 GLN G 238 ASN G 283 GLN G 352 GLN G 728 GLN C 486 ASN C 544 ASN B 52 ASN B 196 ASN A 12 HIS M 119 ASN M 322 HIS ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 GLN K 5 GLN K 82 GLN J 86 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.070217 restraints weight = 39393.335| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.02 r_work: 0.2810 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.249 37927 Z= 0.405 Angle : 2.515 50.695 51444 Z= 1.447 Chirality : 0.449 6.556 5718 Planarity : 0.005 0.063 6398 Dihedral : 9.175 118.931 5727 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.24 % Allowed : 17.40 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.12), residues: 4606 helix: 1.46 (0.10), residues: 2689 sheet: -0.21 (0.29), residues: 306 loop : -0.31 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG N 31 TYR 0.033 0.002 TYR H 242 PHE 0.033 0.002 PHE C 340 TRP 0.028 0.001 TRP N 53 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01161 (37891) covalent geometry : angle 2.19838 (51351) hydrogen bonds : bond 0.05479 ( 1685) hydrogen bonds : angle 4.29394 ( 5055) metal coordination : bond 0.04490 ( 36) metal coordination : angle 28.82497 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 516 time to evaluate : 1.342 Fit side-chains REVERT: F 241 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8549 (tppp) REVERT: G 85 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: G 187 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8151 (pm20) REVERT: G 773 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7535 (pt0) REVERT: G 834 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8187 (mm-40) REVERT: C 127 PHE cc_start: 0.9454 (OUTLIER) cc_final: 0.8483 (t80) REVERT: C 391 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8398 (tp) REVERT: C 600 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.5725 (ptp90) REVERT: B 68 MET cc_start: 0.8155 (ptt) cc_final: 0.7846 (ttp) REVERT: B 146 ASP cc_start: 0.8908 (p0) cc_final: 0.8513 (p0) REVERT: B 202 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: H 13 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8224 (tt) REVERT: A 30 MET cc_start: 0.8638 (ttm) cc_final: 0.8176 (ptm) REVERT: L 581 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8264 (mptt) REVERT: M 109 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8317 (pp) REVERT: K 88 GLN cc_start: 0.8306 (mp10) cc_final: 0.8071 (mm-40) REVERT: K 97 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7767 (pm20) REVERT: K 98 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8019 (mtp) REVERT: J 24 ASN cc_start: 0.8824 (t0) cc_final: 0.8548 (t0) REVERT: J 59 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8545 (t80) outliers start: 85 outliers final: 50 residues processed: 566 average time/residue: 0.7751 time to fit residues: 521.1418 Evaluate side-chains 574 residues out of total 3798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 510 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 386 TRP Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 600 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 102 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 519 VAL Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 265 LYS Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 386 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 460 random chunks: chunk 430 optimal weight: 5.9990 chunk 265 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 356 optimal weight: 0.5980 chunk 314 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 374 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 360 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN G 238 ASN G 283 GLN G 728 GLN B 52 ASN B 196 ASN A 12 HIS M 119 ASN M 322 HIS M 361 GLN N 449 GLN K 5 GLN K 82 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.071447 restraints weight = 39505.930| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.00 r_work: 0.2837 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.248 37927 Z= 0.394 Angle : 2.513 50.656 51444 Z= 1.445 Chirality : 0.447 6.491 5718 Planarity : 0.004 0.065 6398 Dihedral : 9.015 119.794 5727 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.11 % Allowed : 17.53 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.12), residues: 4606 helix: 1.54 (0.10), residues: 2694 sheet: -0.22 (0.29), residues: 308 loop : -0.25 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG N 31 TYR 0.033 0.002 TYR H 242 PHE 0.032 0.001 PHE C 340 TRP 0.029 0.001 TRP N 53 HIS 0.008 0.001 HIS M 322 Details of bonding type rmsd covalent geometry : bond 0.01143 (37891) covalent geometry : angle 2.19355 (51351) hydrogen bonds : bond 0.05087 ( 1685) hydrogen bonds : angle 4.23491 ( 5055) metal coordination : bond 0.03592 ( 36) metal coordination : angle 28.92421 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17845.91 seconds wall clock time: 303 minutes 7.58 seconds (18187.58 seconds total)