Starting phenix.real_space_refine on Sat Mar 7 01:47:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p61_13214/03_2026/7p61_13214.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p61_13214/03_2026/7p61_13214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p61_13214/03_2026/7p61_13214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p61_13214/03_2026/7p61_13214.map" model { file = "/net/cci-nas-00/data/ceres_data/7p61_13214/03_2026/7p61_13214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p61_13214/03_2026/7p61_13214.cif" } resolution = 3.2 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= 0.008 sd= 0.034 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 5 5.49 5 S 265 5.16 5 C 23803 2.51 5 N 6112 2.21 5 O 6472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s 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: 36690 Number of models: 1 Model: "" Number of chains: 20 Chain: "F" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3432 Classifications: {'peptide': 442} Link IDs: {'PCIS': 1, 'PTRANS': 24, '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: {'PTRANS': 9, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4606 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 536} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 177} Chain breaks: 3 Chain: "I" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1157 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 134} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 4525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4525 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 18, 'TRANS': 574} Chain breaks: 3 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 482} Chain: "N" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3630 Classifications: {'peptide': 479} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 458} Chain breaks: 2 Chain: "H" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2449 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 297} Chain breaks: 1 Chain: "A" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 840 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain breaks: 1 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: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1326 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} 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: "L" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "H" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'UQ8': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UQ8:plan-2': 1, 'UQ8:plan-3': 1, 'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1} Unresolved non-hydrogen planarities: 29 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2746 SG CYS F 354 58.000 60.060 186.262 1.00 42.83 S ATOM 2766 SG CYS F 357 60.934 59.643 191.244 1.00 43.36 S ATOM 3087 SG CYS F 398 55.147 56.343 190.926 1.00 47.90 S ATOM 2722 SG CYS F 351 60.044 53.849 187.825 1.00 26.05 S ATOM 4079 SG CYS E 92 66.098 50.835 208.196 1.00 63.34 S ATOM 4113 SG CYS E 97 66.059 51.437 211.778 1.00 79.45 S ATOM 4417 SG CYS E 137 59.892 51.003 210.256 1.00 68.11 S ATOM 5501 SG CYS G 114 70.353 66.642 170.358 1.00 31.78 S ATOM 5441 SG CYS G 105 75.450 70.015 173.023 1.00 50.80 S ATOM 5461 SG CYS G 108 76.392 64.376 170.133 1.00 31.29 S ATOM 5836 SG CYS G 153 69.321 57.637 177.949 1.00 39.44 S ATOM 5884 SG CYS G 159 66.868 53.193 173.811 1.00 21.26 S ATOM 6228 SG CYS G 203 69.376 58.432 171.327 1.00 61.45 S ATOM 6453 SG CYS G 230 68.138 50.539 149.627 1.00 37.10 S ATOM 6738 SG CYS G 265 67.377 46.739 154.933 1.00 43.75 S ATOM 6501 SG CYS G 237 62.450 50.242 152.236 1.00 48.43 S ATOM 6477 SG CYS G 233 64.973 44.887 149.265 1.00 56.23 S ATOM 4902 SG CYS G 36 57.091 59.893 176.516 1.00 24.85 S ATOM 4978 SG CYS G 47 58.671 62.966 177.343 1.00 38.74 S ATOM 5004 SG CYS G 50 52.812 64.900 176.532 1.00 60.43 S ATOM 5153 SG CYS G 69 52.567 61.186 175.934 1.00 44.25 S ATOM 17076 SG CYS B 129 83.831 94.080 149.064 1.00 50.33 S ATOM 16699 SG CYS B 64 88.743 98.202 151.003 1.00 77.93 S ATOM 16693 SG CYS B 63 82.655 99.895 151.658 1.00 88.39 S ATOM 17293 SG CYS B 158 84.932 95.073 155.332 1.00100.64 S ATOM 18320 SG CYS I 99 88.373 86.710 157.085 1.00 44.28 S ATOM 18363 SG CYS I 105 86.341 83.319 162.216 1.00 39.73 S ATOM 18078 SG CYS I 70 82.961 82.998 156.632 1.00 32.10 S ATOM 18392 SG CYS I 109 86.636 77.470 168.439 1.00 21.35 S ATOM 18055 SG CYS I 66 85.155 77.080 162.165 1.00 27.29 S ATOM 18015 SG CYS I 60 89.115 72.572 164.619 1.00 30.11 S ATOM 18033 SG CYS I 63 82.761 72.850 166.416 1.00 15.48 S Time building chain proxies: 8.29, per 1000 atoms: 0.23 Number of scatterers: 36690 At special positions: 0 Unit cell: (152.784, 225.993, 241.908, 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 265 16.00 P 5 15.00 O 6472 8.00 N 6112 7.00 C 23803 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: 3.06 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" SF4 B 301 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " 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="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8554 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 0 sheets defined 52.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 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 removed outlier: 4.041A pdb=" N LEU F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) 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 removed outlier: 3.903A pdb=" N VAL F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) 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: 4.498A 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: 4.552A pdb=" N ILE E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLU E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.143A 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: 4.588A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.646A 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: 5.323A pdb=" N TYR G 272 " --> pdb=" O GLY G 268 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLY G 273 " --> pdb=" O ARG G 269 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR G 274 " --> pdb=" O PHE G 270 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) removed outlier: 4.462A 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: 4.527A pdb=" N GLU G 372 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 4.807A 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: 4.251A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.562A 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 removed outlier: 4.157A pdb=" N LYS G 484 " --> pdb=" O GLU G 480 " (cutoff:3.500A) 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: 5.979A 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: 5.413A pdb=" N GLY G 687 " --> pdb=" O PRO G 683 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE G 688 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS G 689 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 5.405A 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: 5.535A 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 removed outlier: 4.211A pdb=" N ARG G 829 " --> pdb=" O GLU G 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 825 through 829' Processing helix chain 'G' and resid 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: 4.930A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 removed outlier: 5.612A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (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 removed outlier: 4.417A pdb=" N GLU B 67 " --> pdb=" O CYS B 63 " (cutoff:3.500A) 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 removed outlier: 4.668A pdb=" N LEU H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.685A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE H 98 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 137 removed outlier: 5.014A pdb=" N PHE H 119 " --> pdb=" O GLY H 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.285A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU H 160 " --> pdb=" O TYR H 156 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.276A 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: 4.449A pdb=" N CYS H 305 " --> pdb=" O GLY H 301 " (cutoff:3.500A) Proline residue: H 307 - end of helix Processing helix chain 'A' and resid 7 through 36 removed outlier: 4.873A pdb=" N ALA A 11 " --> pdb=" O THR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 89 removed outlier: 3.970A pdb=" N LEU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) 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 removed outlier: 4.201A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) 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 removed outlier: 4.683A pdb=" N GLU L 202 " --> pdb=" O ARG L 198 " (cutoff:3.500A) Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 removed outlier: 6.565A pdb=" N TRP L 217 " --> pdb=" O ASN L 213 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA L 218 " --> pdb=" O MET L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.981A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N MET L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 256 removed outlier: 4.368A pdb=" N ALA L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) 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 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 removed outlier: 4.515A pdb=" N LEU L 491 " --> pdb=" O HIS L 487 " (cutoff:3.500A) 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: 5.317A 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 removed outlier: 6.207A pdb=" N TYR M 221 " --> pdb=" O SER M 217 " (cutoff:3.500A) 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 removed outlier: 4.148A pdb=" N GLN M 416 " --> pdb=" O PHE M 412 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL M 417 " --> pdb=" O GLY M 413 " (cutoff:3.500A) 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: 4.893A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 removed outlier: 4.522A pdb=" N ILE N 9 " --> pdb=" O PRO N 5 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA N 10 " --> pdb=" O GLN N 6 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 4.131A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) 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 removed outlier: 4.133A pdb=" N LYS N 217 " --> pdb=" O GLY N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.661A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 288 removed outlier: 4.593A pdb=" N VAL N 271 " --> pdb=" O GLU N 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 320 through 347 removed outlier: 5.709A 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: 4.110A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 4.391A 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: 5.198A 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 1632 hydrogen bonds defined for protein. 4896 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: 6.29 Time building geometry restraints manager: 4.08 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: 15726 1.42 - 1.64: 21389 1.64 - 1.86: 406 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 37613 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.385 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.374 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.608 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C10 FMN F 502 " pdb=" N1 FMN F 502 " ideal model delta sigma weight residual 1.317 1.378 -0.061 2.00e-02 2.50e+03 9.23e+00 bond pdb=" O13 3PE L 802 " pdb=" P 3PE L 802 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.29e+00 ... (remaining 37608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 50594 3.20 - 6.39: 423 6.39 - 9.59: 90 9.59 - 12.78: 14 12.78 - 15.98: 3 Bond angle restraints: 51124 Sorted by residual: angle pdb=" CA PRO N 5 " pdb=" N PRO N 5 " pdb=" CD PRO N 5 " ideal model delta sigma weight residual 112.00 104.22 7.78 1.40e+00 5.10e-01 3.09e+01 angle pdb=" CB MET M 136 " pdb=" CG MET M 136 " pdb=" SD MET M 136 " ideal model delta sigma weight residual 112.70 128.68 -15.98 3.00e+00 1.11e-01 2.84e+01 angle pdb=" C PRO N 387 " pdb=" N MET N 388 " pdb=" CA MET N 388 " ideal model delta sigma weight residual 121.54 131.49 -9.95 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C PRO C 153 " pdb=" N ASN C 154 " pdb=" CA ASN C 154 " ideal model delta sigma weight residual 122.46 129.13 -6.67 1.41e+00 5.03e-01 2.24e+01 angle pdb=" C SER A 6 " pdb=" N THR A 7 " pdb=" CA THR A 7 " ideal model delta sigma weight residual 121.54 130.28 -8.74 1.91e+00 2.74e-01 2.09e+01 ... (remaining 51119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 20213 21.25 - 42.49: 1543 42.49 - 63.74: 242 63.74 - 84.98: 36 84.98 - 106.23: 11 Dihedral angle restraints: 22045 sinusoidal: 8679 harmonic: 13366 Sorted by residual: dihedral pdb=" CA CYS B 158 " pdb=" C CYS B 158 " pdb=" N PRO B 159 " pdb=" CA PRO B 159 " ideal model delta harmonic sigma weight residual 180.00 -123.07 -56.93 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA GLY I 85 " pdb=" C GLY I 85 " pdb=" N ARG I 86 " pdb=" CA ARG I 86 " ideal model delta harmonic sigma weight residual 180.00 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA PRO F 201 " pdb=" C PRO F 201 " pdb=" N PRO F 202 " pdb=" CA PRO F 202 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 22042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.235: 5725 4.235 - 8.470: 0 8.470 - 12.705: 0 12.705 - 16.941: 0 16.941 - 21.176: 28 Chirality restraints: 5753 Sorted by residual: 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 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE3 SF4 G1001 " pdb=" S1 SF4 G1001 " pdb=" S2 SF4 G1001 " pdb=" S4 SF4 G1001 " both_signs ideal model delta sigma weight residual False -10.55 10.62 -21.17 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 -10.61 21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5750 not shown) Planarity restraints: 6422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ8 H 401 " 0.000 2.00e-02 2.50e+03 5.59e-02 9.39e+01 pdb=" C1M UQ8 H 401 " 0.040 2.00e-02 2.50e+03 pdb=" C2 UQ8 H 401 " -0.038 2.00e-02 2.50e+03 pdb=" C3 UQ8 H 401 " 0.004 2.00e-02 2.50e+03 pdb=" C4 UQ8 H 401 " -0.017 2.00e-02 2.50e+03 pdb=" C5 UQ8 H 401 " -0.013 2.00e-02 2.50e+03 pdb=" C6 UQ8 H 401 " 0.002 2.00e-02 2.50e+03 pdb=" C7 UQ8 H 401 " 0.045 2.00e-02 2.50e+03 pdb=" O2 UQ8 H 401 " -0.103 2.00e-02 2.50e+03 pdb=" O3 UQ8 H 401 " 0.139 2.00e-02 2.50e+03 pdb=" O4 UQ8 H 401 " -0.041 2.00e-02 2.50e+03 pdb=" O5 UQ8 H 401 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 62 " -0.068 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO L 63 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO L 63 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO L 63 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 73 " 0.022 2.00e-02 2.50e+03 2.35e-02 1.39e+01 pdb=" CG TRP H 73 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP H 73 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP H 73 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 73 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP H 73 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 73 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 73 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 73 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP H 73 " -0.007 2.00e-02 2.50e+03 ... (remaining 6419 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 964 2.70 - 3.25: 36054 3.25 - 3.80: 63890 3.80 - 4.35: 82443 4.35 - 4.90: 136216 Nonbonded interactions: 319567 Sorted by model distance: nonbonded pdb=" OG SER E 94 " pdb=" O CYS E 132 " model vdw 2.156 3.040 nonbonded pdb=" O TYR N 159 " pdb=" OG SER N 163 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.212 3.040 nonbonded pdb=" OG SER G 823 " pdb=" O MET G 888 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.257 3.040 ... (remaining 319562 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: 0.290 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 36.890 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.885 37649 Z= 0.287 Angle : 0.837 15.978 51217 Z= 0.425 Chirality : 1.475 21.176 5753 Planarity : 0.007 0.105 6422 Dihedral : 15.158 106.227 13491 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.29 % Allowed : 15.52 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.11), residues: 4629 helix: -0.09 (0.09), residues: 2578 sheet: -0.91 (0.29), residues: 315 loop : -1.64 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 804 TYR 0.037 0.002 TYR M 435 PHE 0.052 0.002 PHE H 31 TRP 0.061 0.001 TRP H 73 HIS 0.012 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.00429 (37613) covalent geometry : angle 0.82664 (51124) hydrogen bonds : bond 0.04555 ( 1632) hydrogen bonds : angle 4.83179 ( 4896) metal coordination : bond 0.24434 ( 36) metal coordination : angle 3.16212 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 599 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: F 420 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7901 (mm-30) REVERT: G 605 ASN cc_start: 0.8878 (m-40) cc_final: 0.8664 (p0) REVERT: C 62 ASP cc_start: 0.8940 (t0) cc_final: 0.8451 (t70) REVERT: C 215 PHE cc_start: 0.8148 (m-10) cc_final: 0.7784 (p90) REVERT: C 599 ASP cc_start: 0.9240 (m-30) cc_final: 0.9015 (m-30) REVERT: B 92 GLN cc_start: 0.8536 (mp10) cc_final: 0.8242 (mp10) REVERT: B 166 MET cc_start: 0.8716 (tpp) cc_final: 0.8444 (tpp) REVERT: I 176 LYS cc_start: 0.8471 (mttp) cc_final: 0.8106 (mttp) REVERT: L 415 MET cc_start: 0.8151 (ttp) cc_final: 0.7805 (ttp) REVERT: M 5 TRP cc_start: 0.7688 (m100) cc_final: 0.6898 (m-10) REVERT: M 371 MET cc_start: 0.8229 (mtm) cc_final: 0.8022 (mtm) REVERT: M 476 VAL cc_start: 0.8664 (t) cc_final: 0.8266 (m) REVERT: H 10 GLU cc_start: 0.8558 (tp30) cc_final: 0.8316 (tp30) REVERT: H 95 LEU cc_start: 0.8005 (tp) cc_final: 0.7789 (tp) REVERT: H 109 VAL cc_start: 0.8241 (m) cc_final: 0.7722 (p) REVERT: K 32 LEU cc_start: 0.8727 (mt) cc_final: 0.8457 (mt) REVERT: J 24 ASN cc_start: 0.8927 (p0) cc_final: 0.8721 (p0) outliers start: 11 outliers final: 3 residues processed: 602 average time/residue: 0.2453 time to fit residues: 238.5734 Evaluate side-chains 548 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 545 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain N residue 82 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 9.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 33 ASN F 142 ASN E 142 ASN G 180 ASN ** G 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 724 HIS G 901 HIS ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN L 2 ASN L 78 ASN L 135 ASN N 7 ASN N 101 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.072533 restraints weight = 64384.593| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.37 r_work: 0.2914 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.253 37649 Z= 0.389 Angle : 2.519 51.086 51217 Z= 1.447 Chirality : 0.443 6.547 5753 Planarity : 0.005 0.102 6422 Dihedral : 6.562 98.070 5216 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.39 % Allowed : 15.04 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.12), residues: 4629 helix: 0.72 (0.10), residues: 2583 sheet: -0.85 (0.29), residues: 327 loop : -1.49 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 87 TYR 0.025 0.001 TYR M 435 PHE 0.026 0.001 PHE N 72 TRP 0.019 0.001 TRP L 143 HIS 0.006 0.001 HIS L 100 Details of bonding type rmsd covalent geometry : bond 0.01140 (37613) covalent geometry : angle 2.19518 (51124) hydrogen bonds : bond 0.03935 ( 1632) hydrogen bonds : angle 4.17789 ( 4896) metal coordination : bond 0.03336 ( 36) metal coordination : angle 29.08708 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 574 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: G 119 MET cc_start: 0.8942 (mmp) cc_final: 0.8734 (mmt) REVERT: G 272 TYR cc_start: 0.8962 (p90) cc_final: 0.8610 (p90) REVERT: C 599 ASP cc_start: 0.8821 (m-30) cc_final: 0.8592 (m-30) REVERT: L 221 MET cc_start: 0.8808 (mmt) cc_final: 0.8399 (mmt) REVERT: L 400 ASP cc_start: 0.7890 (t70) cc_final: 0.7671 (t0) REVERT: M 235 MET cc_start: 0.8615 (ttp) cc_final: 0.8388 (ttm) REVERT: M 323 MET cc_start: 0.8931 (mmp) cc_final: 0.8706 (mmp) REVERT: M 371 MET cc_start: 0.8247 (mtm) cc_final: 0.8031 (mtm) REVERT: M 476 VAL cc_start: 0.8653 (t) cc_final: 0.8269 (m) REVERT: N 76 TYR cc_start: 0.8277 (m-10) cc_final: 0.8067 (m-10) REVERT: N 132 ILE cc_start: 0.8572 (pt) cc_final: 0.8232 (mt) REVERT: N 139 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8527 (mm) REVERT: N 171 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8538 (mt) REVERT: H 10 GLU cc_start: 0.8227 (tp30) cc_final: 0.8006 (tp30) REVERT: K 32 LEU cc_start: 0.8662 (mt) cc_final: 0.8399 (mt) REVERT: J 24 ASN cc_start: 0.8858 (p0) cc_final: 0.8594 (p0) REVERT: J 73 MET cc_start: 0.8649 (ttp) cc_final: 0.8350 (ttp) outliers start: 53 outliers final: 19 residues processed: 609 average time/residue: 0.2381 time to fit residues: 238.0662 Evaluate side-chains 558 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 537 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain A residue 10 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 332 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 chunk 438 optimal weight: 7.9990 chunk 171 optimal weight: 0.0770 chunk 164 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 chunk 312 optimal weight: 0.7980 chunk 360 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 overall best weight: 2.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 33 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 ASN G 238 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 ASN G 397 GLN ** G 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 765 GLN ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN C 483 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.083254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.069848 restraints weight = 63947.222| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.34 r_work: 0.2857 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 37649 Z= 0.395 Angle : 2.518 50.616 51217 Z= 1.447 Chirality : 0.443 6.443 5753 Planarity : 0.004 0.094 6422 Dihedral : 6.242 96.197 5210 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.20 % Allowed : 14.99 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.12), residues: 4629 helix: 1.04 (0.10), residues: 2587 sheet: -0.64 (0.29), residues: 317 loop : -1.34 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 804 TYR 0.022 0.001 TYR M 435 PHE 0.021 0.001 PHE L 341 TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.01152 (37613) covalent geometry : angle 2.19515 (51124) hydrogen bonds : bond 0.04018 ( 1632) hydrogen bonds : angle 4.06427 ( 4896) metal coordination : bond 0.02746 ( 36) metal coordination : angle 29.04940 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 552 time to evaluate : 1.482 Fit side-chains REVERT: G 192 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7384 (pm20) REVERT: G 272 TYR cc_start: 0.8988 (p90) cc_final: 0.8621 (p90) REVERT: G 572 ASP cc_start: 0.8281 (t0) cc_final: 0.8027 (t0) REVERT: C 276 GLU cc_start: 0.7153 (tt0) cc_final: 0.6788 (tt0) REVERT: C 403 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.6874 (tp) REVERT: C 585 ILE cc_start: 0.8700 (tt) cc_final: 0.8317 (mt) REVERT: B 2 ASP cc_start: 0.8132 (p0) cc_final: 0.7893 (p0) REVERT: B 68 MET cc_start: 0.7701 (ptt) cc_final: 0.7349 (ptt) REVERT: I 153 MET cc_start: 0.8863 (mmt) cc_final: 0.7927 (mmt) REVERT: L 400 ASP cc_start: 0.7927 (t70) cc_final: 0.7727 (t0) REVERT: L 432 MET cc_start: 0.8738 (tmm) cc_final: 0.8536 (ttp) REVERT: M 136 MET cc_start: 0.8873 (mmm) cc_final: 0.8599 (mmp) REVERT: M 235 MET cc_start: 0.8641 (ttp) cc_final: 0.8392 (ttm) REVERT: M 370 ASP cc_start: 0.8753 (t70) cc_final: 0.8505 (t0) REVERT: M 476 VAL cc_start: 0.8776 (t) cc_final: 0.8400 (m) REVERT: N 132 ILE cc_start: 0.8589 (pt) cc_final: 0.8317 (mt) REVERT: N 242 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8747 (pp) REVERT: H 10 GLU cc_start: 0.8194 (tp30) cc_final: 0.7948 (tp30) REVERT: H 74 ILE cc_start: 0.7389 (mm) cc_final: 0.7189 (tp) REVERT: H 107 TRP cc_start: 0.8509 (m100) cc_final: 0.8260 (m100) REVERT: J 59 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8501 (t80) outliers start: 84 outliers final: 41 residues processed: 607 average time/residue: 0.2286 time to fit residues: 227.4849 Evaluate side-chains 580 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 535 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 389 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 436 optimal weight: 0.0370 chunk 129 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 110 HIS F 400 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 HIS ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 ASN G 607 HIS G 765 GLN ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS C 319 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN L 270 HIS M 159 HIS H 214 GLN H 226 HIS ** J 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.065320 restraints weight = 62959.012| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.32 r_work: 0.2759 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 37649 Z= 0.418 Angle : 2.536 50.696 51217 Z= 1.454 Chirality : 0.443 6.412 5753 Planarity : 0.005 0.098 6422 Dihedral : 6.186 90.172 5210 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.85 % Allowed : 15.15 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.12), residues: 4629 helix: 1.07 (0.10), residues: 2603 sheet: -0.60 (0.29), residues: 310 loop : -1.26 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 19 TYR 0.020 0.002 TYR M 435 PHE 0.033 0.002 PHE C 215 TRP 0.019 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01195 (37613) covalent geometry : angle 2.21199 (51124) hydrogen bonds : bond 0.04517 ( 1632) hydrogen bonds : angle 4.14724 ( 4896) metal coordination : bond 0.02754 ( 36) metal coordination : angle 29.18557 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 542 time to evaluate : 1.407 Fit side-chains REVERT: F 309 MET cc_start: 0.9240 (mmm) cc_final: 0.8938 (mmm) REVERT: F 434 ASN cc_start: 0.8566 (t0) cc_final: 0.8124 (t0) REVERT: G 70 MET cc_start: 0.9057 (mmm) cc_final: 0.8853 (mmm) REVERT: G 485 ILE cc_start: 0.9278 (mm) cc_final: 0.9010 (mt) REVERT: G 572 ASP cc_start: 0.8425 (t0) cc_final: 0.8224 (t0) REVERT: G 644 LYS cc_start: 0.8718 (mtmp) cc_final: 0.8501 (mtmm) REVERT: C 344 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7785 (mm-40) REVERT: C 403 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7009 (tp) REVERT: C 528 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7834 (mtt) REVERT: C 585 ILE cc_start: 0.8749 (tt) cc_final: 0.8465 (mt) REVERT: B 2 ASP cc_start: 0.8207 (p0) cc_final: 0.7840 (p0) REVERT: B 47 ASN cc_start: 0.8844 (m-40) cc_final: 0.8614 (m110) REVERT: B 189 ASP cc_start: 0.8510 (t0) cc_final: 0.8305 (t0) REVERT: I 153 MET cc_start: 0.8889 (mmt) cc_final: 0.7912 (mmt) REVERT: L 415 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7498 (ttp) REVERT: L 430 PHE cc_start: 0.8464 (m-80) cc_final: 0.8107 (m-80) REVERT: M 145 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8736 (tmm) REVERT: M 235 MET cc_start: 0.8608 (ttp) cc_final: 0.8342 (ttm) REVERT: M 370 ASP cc_start: 0.8779 (t70) cc_final: 0.8280 (t0) REVERT: N 132 ILE cc_start: 0.8633 (pt) cc_final: 0.8413 (mt) REVERT: N 139 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8646 (mt) REVERT: H 10 GLU cc_start: 0.8179 (tp30) cc_final: 0.7968 (tp30) REVERT: H 107 TRP cc_start: 0.8583 (m100) cc_final: 0.8375 (m100) REVERT: H 181 ASN cc_start: 0.8376 (m-40) cc_final: 0.8035 (m-40) REVERT: H 241 GLU cc_start: 0.7266 (tt0) cc_final: 0.7031 (tt0) REVERT: J 59 TYR cc_start: 0.9254 (OUTLIER) cc_final: 0.8674 (t80) outliers start: 109 outliers final: 65 residues processed: 615 average time/residue: 0.2287 time to fit residues: 231.0305 Evaluate side-chains 581 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 510 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 392 VAL Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 258 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 chunk 457 optimal weight: 6.9990 chunk 387 optimal weight: 7.9990 chunk 370 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 ASN ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN C 544 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN H 226 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.076283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.063040 restraints weight = 62500.383| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.21 r_work: 0.2712 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.241 37649 Z= 0.453 Angle : 2.549 50.721 51217 Z= 1.460 Chirality : 0.445 6.443 5753 Planarity : 0.005 0.098 6422 Dihedral : 6.262 88.088 5210 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.64 % Allowed : 14.65 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.12), residues: 4629 helix: 0.99 (0.10), residues: 2597 sheet: -0.68 (0.29), residues: 323 loop : -1.19 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 269 TYR 0.021 0.002 TYR C 100 PHE 0.041 0.002 PHE C 215 TRP 0.016 0.001 TRP N 53 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01259 (37613) covalent geometry : angle 2.22688 (51124) hydrogen bonds : bond 0.04893 ( 1632) hydrogen bonds : angle 4.31347 ( 4896) metal coordination : bond 0.03056 ( 36) metal coordination : angle 29.21009 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 517 time to evaluate : 1.362 Fit side-chains REVERT: F 309 MET cc_start: 0.9240 (mmm) cc_final: 0.8979 (mmm) REVERT: F 312 GLU cc_start: 0.8357 (pm20) cc_final: 0.8153 (pm20) REVERT: F 408 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9036 (tp) REVERT: F 434 ASN cc_start: 0.8689 (t0) cc_final: 0.8369 (t0) REVERT: G 98 MET cc_start: 0.8727 (mmm) cc_final: 0.7899 (mmt) REVERT: G 293 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8946 (pt) REVERT: G 485 ILE cc_start: 0.9272 (mm) cc_final: 0.9015 (mt) REVERT: G 605 ASN cc_start: 0.8609 (p0) cc_final: 0.8277 (p0) REVERT: G 644 LYS cc_start: 0.8698 (mtmp) cc_final: 0.8472 (mtmm) REVERT: G 870 THR cc_start: 0.8987 (p) cc_final: 0.8761 (p) REVERT: C 528 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7990 (mmt) REVERT: C 555 MET cc_start: 0.8929 (mtm) cc_final: 0.8721 (mtt) REVERT: C 585 ILE cc_start: 0.8721 (tt) cc_final: 0.8491 (mt) REVERT: B 2 ASP cc_start: 0.8298 (p0) cc_final: 0.8063 (p0) REVERT: B 189 ASP cc_start: 0.8581 (t0) cc_final: 0.8369 (t0) REVERT: I 153 MET cc_start: 0.8921 (mmt) cc_final: 0.7896 (mmt) REVERT: L 88 MET cc_start: 0.8830 (mmm) cc_final: 0.8344 (mmm) REVERT: L 407 MET cc_start: 0.7627 (tpt) cc_final: 0.7191 (tpt) REVERT: L 415 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7970 (ttp) REVERT: L 430 PHE cc_start: 0.8500 (m-80) cc_final: 0.8155 (m-80) REVERT: M 22 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.4421 (ptp-170) REVERT: M 145 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8793 (tmm) REVERT: M 235 MET cc_start: 0.8598 (ttp) cc_final: 0.8319 (ttm) REVERT: M 370 ASP cc_start: 0.8847 (t70) cc_final: 0.8336 (t0) REVERT: M 440 LEU cc_start: 0.8926 (mt) cc_final: 0.8707 (mt) REVERT: N 74 MET cc_start: 0.8727 (ttm) cc_final: 0.8469 (ttm) REVERT: N 132 ILE cc_start: 0.8713 (pt) cc_final: 0.8483 (mt) REVERT: N 139 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8693 (mt) REVERT: N 324 GLU cc_start: 0.8525 (tt0) cc_final: 0.8302 (tt0) REVERT: N 482 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7217 (mmm) REVERT: H 63 ASP cc_start: 0.8279 (t0) cc_final: 0.8035 (t0) REVERT: H 94 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8407 (mm) REVERT: H 147 MET cc_start: 0.8820 (mmm) cc_final: 0.8496 (mmp) REVERT: H 220 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6579 (mm-30) REVERT: H 241 GLU cc_start: 0.7538 (tt0) cc_final: 0.7295 (tt0) REVERT: H 278 PHE cc_start: 0.8696 (m-80) cc_final: 0.8345 (m-80) REVERT: J 59 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.8751 (t80) outliers start: 139 outliers final: 86 residues processed: 615 average time/residue: 0.2350 time to fit residues: 236.8834 Evaluate side-chains 583 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 487 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 93 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 270 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 chunk 325 optimal weight: 8.9990 chunk 384 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 chunk 390 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 142 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN H 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.077597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.064133 restraints weight = 62540.380| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.29 r_work: 0.2732 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 37649 Z= 0.408 Angle : 2.533 50.713 51217 Z= 1.452 Chirality : 0.443 6.391 5753 Planarity : 0.004 0.100 6422 Dihedral : 6.021 88.881 5210 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.35 % Allowed : 15.31 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.12), residues: 4629 helix: 1.15 (0.10), residues: 2602 sheet: -0.71 (0.29), residues: 319 loop : -1.16 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 63 TYR 0.022 0.002 TYR M 435 PHE 0.038 0.002 PHE C 215 TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01177 (37613) covalent geometry : angle 2.20692 (51124) hydrogen bonds : bond 0.04466 ( 1632) hydrogen bonds : angle 4.20011 ( 4896) metal coordination : bond 0.02418 ( 36) metal coordination : angle 29.27942 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 506 time to evaluate : 1.487 Fit side-chains REVERT: F 309 MET cc_start: 0.9230 (mmm) cc_final: 0.8962 (mmm) REVERT: F 434 ASN cc_start: 0.8602 (t0) cc_final: 0.8308 (t0) REVERT: E 82 GLN cc_start: 0.9232 (mm-40) cc_final: 0.9019 (mt0) REVERT: G 98 MET cc_start: 0.8699 (mmm) cc_final: 0.7962 (mmt) REVERT: G 293 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8884 (pt) REVERT: G 485 ILE cc_start: 0.9247 (mm) cc_final: 0.8970 (mt) REVERT: G 644 LYS cc_start: 0.8694 (mtmp) cc_final: 0.8476 (mtmm) REVERT: G 870 THR cc_start: 0.8978 (p) cc_final: 0.8750 (p) REVERT: C 528 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7930 (mmt) REVERT: C 555 MET cc_start: 0.8990 (mtm) cc_final: 0.8720 (mtt) REVERT: C 585 ILE cc_start: 0.8705 (tt) cc_final: 0.8484 (mt) REVERT: B 2 ASP cc_start: 0.8356 (p0) cc_final: 0.8095 (p0) REVERT: B 22 GLN cc_start: 0.8579 (mt0) cc_final: 0.8373 (mt0) REVERT: I 153 MET cc_start: 0.8990 (mmt) cc_final: 0.7955 (mmt) REVERT: L 88 MET cc_start: 0.8866 (mmm) cc_final: 0.8489 (mmm) REVERT: L 345 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7784 (mp) REVERT: L 407 MET cc_start: 0.7785 (tpt) cc_final: 0.7489 (tpt) REVERT: L 415 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7779 (ttp) REVERT: L 430 PHE cc_start: 0.8410 (m-80) cc_final: 0.8066 (m-80) REVERT: M 22 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.4348 (ptp-170) REVERT: M 145 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8810 (tmm) REVERT: M 235 MET cc_start: 0.8572 (ttp) cc_final: 0.8316 (ttm) REVERT: M 370 ASP cc_start: 0.8844 (t70) cc_final: 0.8337 (t0) REVERT: N 139 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8660 (mt) REVERT: H 94 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8375 (mm) REVERT: H 220 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6447 (mm-30) REVERT: H 241 GLU cc_start: 0.7527 (tt0) cc_final: 0.7253 (tt0) REVERT: J 59 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8708 (t80) outliers start: 128 outliers final: 76 residues processed: 597 average time/residue: 0.2263 time to fit residues: 222.8922 Evaluate side-chains 572 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 487 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain G residue 57 ASN Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 135 ASN Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 345 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 93 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 404 optimal weight: 9.9990 chunk 145 optimal weight: 0.1980 chunk 54 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 332 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 435 optimal weight: 5.9990 chunk 380 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 142 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 GLN H 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.077337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.064289 restraints weight = 62304.795| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.20 r_work: 0.2740 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 37649 Z= 0.412 Angle : 2.536 50.695 51217 Z= 1.453 Chirality : 0.443 6.397 5753 Planarity : 0.004 0.097 6422 Dihedral : 5.985 87.227 5210 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.11 % Allowed : 15.99 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 4629 helix: 1.16 (0.10), residues: 2605 sheet: -0.70 (0.29), residues: 319 loop : -1.14 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 63 TYR 0.025 0.002 TYR C 277 PHE 0.051 0.002 PHE N 72 TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01185 (37613) covalent geometry : angle 2.20991 (51124) hydrogen bonds : bond 0.04476 ( 1632) hydrogen bonds : angle 4.19176 ( 4896) metal coordination : bond 0.02435 ( 36) metal coordination : angle 29.25392 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 494 time to evaluate : 1.522 Fit side-chains REVERT: F 220 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: F 387 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8545 (tp) REVERT: F 434 ASN cc_start: 0.8643 (t0) cc_final: 0.8371 (t0) REVERT: G 293 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8891 (pt) REVERT: G 485 ILE cc_start: 0.9238 (mm) cc_final: 0.8987 (mt) REVERT: G 644 LYS cc_start: 0.8693 (mtmp) cc_final: 0.8474 (mtmm) REVERT: G 870 THR cc_start: 0.8952 (p) cc_final: 0.8658 (p) REVERT: C 528 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7865 (mmt) REVERT: C 585 ILE cc_start: 0.8691 (tt) cc_final: 0.8474 (mt) REVERT: B 2 ASP cc_start: 0.8326 (p0) cc_final: 0.8006 (p0) REVERT: B 22 GLN cc_start: 0.8555 (mt0) cc_final: 0.8316 (mt0) REVERT: I 153 MET cc_start: 0.8973 (mmt) cc_final: 0.8051 (mmt) REVERT: L 88 MET cc_start: 0.8863 (mmm) cc_final: 0.8477 (mmm) REVERT: L 345 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7721 (mp) REVERT: L 430 PHE cc_start: 0.8372 (m-80) cc_final: 0.8059 (m-80) REVERT: M 22 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.4349 (ptp-170) REVERT: M 145 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8810 (tmm) REVERT: M 235 MET cc_start: 0.8578 (ttp) cc_final: 0.8311 (ttm) REVERT: M 370 ASP cc_start: 0.8844 (t70) cc_final: 0.8335 (t0) REVERT: N 139 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8661 (mt) REVERT: H 94 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8348 (mm) REVERT: H 147 MET cc_start: 0.8760 (mmm) cc_final: 0.8436 (mmp) REVERT: H 220 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6604 (mm-30) REVERT: H 241 GLU cc_start: 0.7527 (tt0) cc_final: 0.7232 (tt0) REVERT: H 296 GLN cc_start: 0.7745 (mp10) cc_final: 0.7480 (mp10) REVERT: J 59 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8695 (t80) REVERT: J 80 GLU cc_start: 0.7016 (mp0) cc_final: 0.6692 (mp0) outliers start: 119 outliers final: 82 residues processed: 578 average time/residue: 0.2229 time to fit residues: 212.4649 Evaluate side-chains 576 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 484 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 345 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 277 optimal weight: 10.0000 chunk 411 optimal weight: 7.9990 chunk 414 optimal weight: 0.7980 chunk 296 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 385 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 307 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 142 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.076999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.063862 restraints weight = 62005.893| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.21 r_work: 0.2731 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 37649 Z= 0.417 Angle : 2.538 50.663 51217 Z= 1.454 Chirality : 0.443 6.403 5753 Planarity : 0.004 0.099 6422 Dihedral : 5.994 85.732 5210 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.14 % Allowed : 16.09 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.12), residues: 4629 helix: 1.17 (0.10), residues: 2604 sheet: -0.68 (0.29), residues: 319 loop : -1.11 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 87 TYR 0.028 0.002 TYR C 277 PHE 0.051 0.002 PHE N 72 TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01194 (37613) covalent geometry : angle 2.21263 (51124) hydrogen bonds : bond 0.04519 ( 1632) hydrogen bonds : angle 4.20783 ( 4896) metal coordination : bond 0.02602 ( 36) metal coordination : angle 29.26603 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 493 time to evaluate : 1.497 Fit side-chains REVERT: F 220 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: F 285 LEU cc_start: 0.8673 (mt) cc_final: 0.8442 (mp) REVERT: F 387 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8578 (tp) REVERT: F 434 ASN cc_start: 0.8665 (t0) cc_final: 0.8412 (t0) REVERT: G 293 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8957 (pt) REVERT: G 485 ILE cc_start: 0.9217 (mm) cc_final: 0.8968 (mt) REVERT: G 644 LYS cc_start: 0.8711 (mtmp) cc_final: 0.8496 (mtmm) REVERT: G 811 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8624 (ttmm) REVERT: C 528 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7912 (mmt) REVERT: C 585 ILE cc_start: 0.8695 (tt) cc_final: 0.8486 (mt) REVERT: B 2 ASP cc_start: 0.8356 (p0) cc_final: 0.8069 (p0) REVERT: B 22 GLN cc_start: 0.8542 (mt0) cc_final: 0.8312 (mt0) REVERT: I 153 MET cc_start: 0.8994 (mmt) cc_final: 0.8099 (mmt) REVERT: L 88 MET cc_start: 0.8850 (mmm) cc_final: 0.8452 (mmm) REVERT: L 345 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7766 (mp) REVERT: L 415 MET cc_start: 0.8027 (ttp) cc_final: 0.7678 (ttp) REVERT: L 430 PHE cc_start: 0.8402 (m-80) cc_final: 0.8084 (m-80) REVERT: M 22 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.4314 (ptp-170) REVERT: M 145 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8820 (tmm) REVERT: M 370 ASP cc_start: 0.8851 (t70) cc_final: 0.8327 (t0) REVERT: N 139 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8671 (mt) REVERT: N 223 PHE cc_start: 0.9521 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: H 94 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8329 (mm) REVERT: H 147 MET cc_start: 0.8797 (mmm) cc_final: 0.8462 (mmp) REVERT: H 220 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6686 (mm-30) REVERT: H 241 GLU cc_start: 0.7587 (tt0) cc_final: 0.7294 (tt0) REVERT: J 59 TYR cc_start: 0.9239 (OUTLIER) cc_final: 0.8698 (t80) REVERT: J 80 GLU cc_start: 0.7051 (mp0) cc_final: 0.6697 (mp0) outliers start: 120 outliers final: 91 residues processed: 580 average time/residue: 0.2286 time to fit residues: 217.4695 Evaluate side-chains 583 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 480 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 811 LYS Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 345 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 223 PHE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 165 optimal weight: 8.9990 chunk 345 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 315 optimal weight: 0.9980 chunk 235 optimal weight: 7.9990 chunk 386 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 793 ASN ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN H 226 HIS J 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.064995 restraints weight = 62251.645| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.28 r_work: 0.2754 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 37649 Z= 0.397 Angle : 2.532 50.673 51217 Z= 1.451 Chirality : 0.442 6.379 5753 Planarity : 0.004 0.095 6422 Dihedral : 5.883 84.283 5210 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.72 % Allowed : 16.95 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.12), residues: 4629 helix: 1.27 (0.10), residues: 2607 sheet: -0.58 (0.29), residues: 314 loop : -1.09 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 87 TYR 0.030 0.001 TYR C 277 PHE 0.049 0.001 PHE N 72 TRP 0.018 0.001 TRP L 143 HIS 0.004 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01157 (37613) covalent geometry : angle 2.20505 (51124) hydrogen bonds : bond 0.04236 ( 1632) hydrogen bonds : angle 4.12934 ( 4896) metal coordination : bond 0.02175 ( 36) metal coordination : angle 29.28100 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 511 time to evaluate : 1.407 Fit side-chains REVERT: F 285 LEU cc_start: 0.8565 (mt) cc_final: 0.8356 (mp) REVERT: F 387 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8545 (tp) REVERT: F 434 ASN cc_start: 0.8616 (t0) cc_final: 0.8355 (t0) REVERT: G 293 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8945 (pt) REVERT: G 485 ILE cc_start: 0.9200 (mm) cc_final: 0.8950 (mt) REVERT: G 644 LYS cc_start: 0.8695 (mtmp) cc_final: 0.8475 (mtmm) REVERT: C 585 ILE cc_start: 0.8666 (tt) cc_final: 0.8450 (mt) REVERT: B 2 ASP cc_start: 0.8362 (p0) cc_final: 0.8027 (p0) REVERT: I 83 LYS cc_start: 0.8646 (ptpt) cc_final: 0.8443 (ptpt) REVERT: I 153 MET cc_start: 0.8985 (mmt) cc_final: 0.8122 (mmt) REVERT: L 88 MET cc_start: 0.8810 (mmm) cc_final: 0.8456 (mmm) REVERT: L 326 GLN cc_start: 0.8930 (mp10) cc_final: 0.8411 (mp10) REVERT: L 345 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7770 (mp) REVERT: L 430 PHE cc_start: 0.8283 (m-80) cc_final: 0.8020 (m-80) REVERT: M 22 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.4381 (ptp-170) REVERT: M 145 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8823 (tmm) REVERT: M 235 MET cc_start: 0.8554 (ttp) cc_final: 0.8304 (ttm) REVERT: M 370 ASP cc_start: 0.8897 (t70) cc_final: 0.8370 (t0) REVERT: N 139 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8637 (mt) REVERT: H 94 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8195 (mm) REVERT: H 147 MET cc_start: 0.8782 (mmm) cc_final: 0.8384 (mmp) REVERT: H 220 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6579 (mm-30) REVERT: H 241 GLU cc_start: 0.7555 (tt0) cc_final: 0.7294 (tt0) REVERT: H 296 GLN cc_start: 0.7713 (mp10) cc_final: 0.7493 (mp10) REVERT: J 59 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8627 (t80) REVERT: J 80 GLU cc_start: 0.7083 (mp0) cc_final: 0.6706 (mp0) REVERT: J 82 GLU cc_start: 0.7496 (pt0) cc_final: 0.7200 (tt0) outliers start: 104 outliers final: 81 residues processed: 584 average time/residue: 0.2239 time to fit residues: 214.8296 Evaluate side-chains 572 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 483 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 345 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 102 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 324 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 359 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 454 optimal weight: 9.9990 chunk 314 optimal weight: 8.9990 chunk 383 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 793 ASN ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 ASN H 181 ASN H 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.075269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.061712 restraints weight = 62343.113| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.25 r_work: 0.2681 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.240 37649 Z= 0.466 Angle : 2.558 50.743 51217 Z= 1.463 Chirality : 0.445 6.450 5753 Planarity : 0.005 0.102 6422 Dihedral : 6.142 85.495 5210 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.69 % Allowed : 17.24 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.12), residues: 4629 helix: 1.05 (0.10), residues: 2607 sheet: -0.74 (0.28), residues: 330 loop : -1.04 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 269 TYR 0.033 0.002 TYR C 277 PHE 0.055 0.002 PHE N 72 TRP 0.022 0.002 TRP N 53 HIS 0.008 0.002 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01288 (37613) covalent geometry : angle 2.23502 (51124) hydrogen bonds : bond 0.04984 ( 1632) hydrogen bonds : angle 4.34745 ( 4896) metal coordination : bond 0.03104 ( 36) metal coordination : angle 29.30565 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9258 Ramachandran restraints generated. 4629 Oldfield, 0 Emsley, 4629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 485 time to evaluate : 1.298 Fit side-chains REVERT: F 220 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: F 285 LEU cc_start: 0.8720 (mt) cc_final: 0.8456 (mp) REVERT: F 387 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8599 (tp) REVERT: F 434 ASN cc_start: 0.8727 (t0) cc_final: 0.8516 (t0) REVERT: G 288 ARG cc_start: 0.7899 (ptp90) cc_final: 0.7209 (ptp90) REVERT: G 293 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9080 (pt) REVERT: G 485 ILE cc_start: 0.9241 (mm) cc_final: 0.9010 (mt) REVERT: G 605 ASN cc_start: 0.8677 (p0) cc_final: 0.8298 (p0) REVERT: G 644 LYS cc_start: 0.8783 (mtmp) cc_final: 0.8581 (mtmm) REVERT: C 403 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7990 (tp) REVERT: B 2 ASP cc_start: 0.8366 (p0) cc_final: 0.7982 (p0) REVERT: I 83 LYS cc_start: 0.8698 (ptpt) cc_final: 0.8494 (ptpt) REVERT: I 153 MET cc_start: 0.9004 (mmt) cc_final: 0.8088 (mmt) REVERT: L 88 MET cc_start: 0.8874 (mmm) cc_final: 0.8408 (mmm) REVERT: L 326 GLN cc_start: 0.9000 (mp10) cc_final: 0.8628 (mp10) REVERT: L 430 PHE cc_start: 0.8409 (m-80) cc_final: 0.8121 (m-80) REVERT: M 22 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.4487 (ptp-170) REVERT: M 145 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8851 (tmm) REVERT: M 370 ASP cc_start: 0.8880 (t70) cc_final: 0.8357 (t0) REVERT: N 139 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8672 (mt) REVERT: N 379 MET cc_start: 0.8933 (mmt) cc_final: 0.8686 (mmt) REVERT: H 94 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8460 (mm) REVERT: H 147 MET cc_start: 0.8852 (mmm) cc_final: 0.8510 (mmt) REVERT: H 207 CYS cc_start: 0.7575 (t) cc_final: 0.6986 (t) REVERT: H 220 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6745 (mm-30) REVERT: H 241 GLU cc_start: 0.7741 (tt0) cc_final: 0.7399 (tt0) REVERT: H 296 GLN cc_start: 0.7842 (mp10) cc_final: 0.7563 (mp10) REVERT: J 59 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.8790 (t80) REVERT: J 80 GLU cc_start: 0.7061 (mp0) cc_final: 0.6739 (mp0) REVERT: J 82 GLU cc_start: 0.7438 (pt0) cc_final: 0.7229 (tt0) outliers start: 103 outliers final: 82 residues processed: 564 average time/residue: 0.2219 time to fit residues: 204.5367 Evaluate side-chains 575 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 484 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 858 THR Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 107 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain M residue 22 ARG Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 309 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 443 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 307 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 793 ASN ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 ASN H 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.078897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.065572 restraints weight = 61990.635| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.29 r_work: 0.2761 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 37649 Z= 0.394 Angle : 2.534 50.688 51217 Z= 1.452 Chirality : 0.441 6.369 5753 Planarity : 0.004 0.094 6422 Dihedral : 5.884 83.064 5210 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.28 % Allowed : 17.95 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.12), residues: 4629 helix: 1.28 (0.10), residues: 2608 sheet: -0.63 (0.29), residues: 325 loop : -1.04 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 87 TYR 0.025 0.001 TYR C 277 PHE 0.049 0.001 PHE N 72 TRP 0.019 0.001 TRP L 143 HIS 0.006 0.001 HIS L 334 Details of bonding type rmsd covalent geometry : bond 0.01153 (37613) covalent geometry : angle 2.20624 (51124) hydrogen bonds : bond 0.04172 ( 1632) hydrogen bonds : angle 4.14332 ( 4896) metal coordination : bond 0.02065 ( 36) metal coordination : angle 29.34754 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11026.69 seconds wall clock time: 188 minutes 56.49 seconds (11336.49 seconds total)