Starting phenix.real_space_refine on Mon Jul 6 15:25:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p61_13214/07_2026/7p61_13214.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p61_13214/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7p61_13214/07_2026/7p61_13214.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p61_13214/07_2026/7p61_13214.cif" model { file = "/net/cci-nas-00/data/ceres_data/7p61_13214/07_2026/7p61_13214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p61_13214/07_2026/7p61_13214.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p61_13214/07_2026/7p61_13214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p61_13214/07_2026/7p61_13214.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.30, per 1000 atoms: 0.20 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: 3.33 Conformation dependent library (CDL) restraints added in 1.6 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: 0.79 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: 6.48 Time building geometry restraints manager: 4.38 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=" 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 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" O3 NAI F 503 " pdb=" PN NAI F 503 " ideal model delta sigma weight residual 1.644 1.592 0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" O11 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.644 1.596 0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" O11 3PE L 802 " pdb=" P 3PE L 802 " ideal model delta sigma weight residual 1.644 1.597 0.047 2.00e-02 2.50e+03 5.59e+00 ... (remaining 37608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 50605 3.20 - 6.39: 415 6.39 - 9.59: 87 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 - 33.69: 21343 33.69 - 67.38: 587 67.38 - 101.06: 38 101.06 - 134.75: 0 134.75 - 168.44: 1 Dihedral angle restraints: 21969 sinusoidal: 8603 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=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 89.15 168.44 1 2.00e+01 2.50e-03 4.75e+01 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 ... (remaining 21966 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: 6421 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 6418 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.890 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 36.960 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 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: 0.020 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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= 0.283 Angle : 0.832 15.978 51217 Z= 0.424 Chirality : 1.475 21.176 5753 Planarity : 0.007 0.105 6421 Dihedral : 15.068 168.439 13415 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/Z covalent geometry : bond 0.00418 / 0.19 (37613) covalent geometry : angle 0.82219 / 0.42 (51124) hydrogen bonds : bond 0.04555 / 3.05 ( 1632) hydrogen bonds : angle 4.83179 / 3.38 ( 4896) metal coordination : bond 0.24434 / 17.16 ( 36) metal coordination : angle 3.16212 / 1.98 ( 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 : 1.174 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: 0.2265 time to fit residues: 220.3989 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 : 1.371 ------------------------------------------------------------------------------- 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... 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 = 0.085876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.072662 restraints weight = 64438.661| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.38 r_work: 0.2914 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.257 37649 Z= 0.392 Angle : 2.519 50.989 51217 Z= 1.448 Chirality : 0.442 6.521 5753 Planarity : 0.005 0.103 6421 Dihedral : 6.054 169.720 5140 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.36 % Allowed : 15.23 % Favored : 83.41 % 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: -0.35 (0.12), residues: 4629 helix: 0.70 (0.10), residues: 2582 sheet: -0.86 (0.29), residues: 319 loop : -1.49 (0.14), residues: 1728 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 0.025 0.001 PHE N 72 TRP 0.018 0.001 TRP L 143 HIS 0.006 0.001 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.01149 / 0.39 (37613) covalent geometry : angle 2.19636 / 1.45 (51124) hydrogen bonds : bond 0.03946 / 2.64 ( 1632) hydrogen bonds : angle 4.19307 / 2.93 ( 4896) metal coordination : bond 0.03800 / 2.60 ( 36) metal coordination : angle 29.01953 / 19.60 ( 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 621 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 569 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: G 119 MET cc_start: 0.8936 (mmp) cc_final: 0.8726 (mmt) REVERT: G 272 TYR cc_start: 0.8961 (p90) cc_final: 0.8611 (p90) REVERT: C 599 ASP cc_start: 0.8819 (m-30) cc_final: 0.8590 (m-30) REVERT: L 221 MET cc_start: 0.8811 (mmt) cc_final: 0.8401 (mmt) REVERT: L 400 ASP cc_start: 0.7906 (t70) cc_final: 0.7685 (t0) REVERT: L 415 MET cc_start: 0.7884 (ttp) cc_final: 0.7665 (ttp) REVERT: M 235 MET cc_start: 0.8612 (ttp) cc_final: 0.8390 (ttm) REVERT: M 323 MET cc_start: 0.8936 (mmp) cc_final: 0.8708 (mmp) REVERT: M 371 MET cc_start: 0.8243 (mtm) cc_final: 0.8024 (mtm) REVERT: M 476 VAL cc_start: 0.8651 (t) cc_final: 0.8269 (m) REVERT: N 76 TYR cc_start: 0.8267 (m-10) cc_final: 0.8033 (m-10) REVERT: N 132 ILE cc_start: 0.8574 (pt) cc_final: 0.8222 (mt) REVERT: N 171 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8539 (mt) REVERT: H 10 GLU cc_start: 0.8190 (tp30) cc_final: 0.7944 (tp30) REVERT: K 32 LEU cc_start: 0.8658 (mt) cc_final: 0.8399 (mt) REVERT: J 24 ASN cc_start: 0.8862 (p0) cc_final: 0.8594 (p0) REVERT: J 73 MET cc_start: 0.8649 (ttp) cc_final: 0.8351 (ttp) REVERT: J 80 GLU cc_start: 0.6693 (mp0) cc_final: 0.6493 (mp0) outliers start: 52 outliers final: 20 residues processed: 603 average time/residue: 0.2106 time to fit residues: 208.3616 Evaluate side-chains 555 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 534 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 L residue 487 HIS Chi-restraints excluded: chain M residue 38 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: 9.9990 chunk 254 optimal weight: 7.9990 chunk 438 optimal weight: 8.9990 chunk 171 optimal weight: 0.4980 chunk 164 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 344 optimal weight: 7.9990 chunk 386 optimal weight: 7.9990 chunk 312 optimal weight: 0.8980 chunk 360 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 33 ASN F 400 HIS ** 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 465 HIS G 607 HIS G 765 GLN ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN C 252 HIS C 483 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN M 159 HIS H 226 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.079880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.066311 restraints weight = 63631.578| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.33 r_work: 0.2782 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1597 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= 0.420 Angle : 2.532 50.767 51217 Z= 1.453 Chirality : 0.445 6.443 5753 Planarity : 0.005 0.097 6421 Dihedral : 6.097 173.900 5134 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.51 % Allowed : 14.84 % Favored : 82.65 % 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: -0.01 (0.12), residues: 4629 helix: 0.96 (0.10), residues: 2588 sheet: -0.68 (0.29), residues: 312 loop : -1.34 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 804 TYR 0.020 0.002 TYR M 435 PHE 0.023 0.002 PHE I 101 TRP 0.016 0.001 TRP L 143 HIS 0.009 0.001 HIS F 431 Details of bonding type rmsd/Z covalent geometry : bond 0.01194 / 0.42 (37613) covalent geometry : angle 2.20957 / 1.45 (51124) hydrogen bonds : bond 0.04494 / 3.02 ( 1632) hydrogen bonds : angle 4.17748 / 2.92 ( 4896) metal coordination : bond 0.03145 / 2.02 ( 36) metal coordination : angle 29.08699 / 19.51 ( 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 641 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 545 time to evaluate : 1.345 Fit side-chains REVERT: G 70 MET cc_start: 0.9093 (mmm) cc_final: 0.8826 (mmm) REVERT: G 192 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: G 485 ILE cc_start: 0.9261 (mm) cc_final: 0.8966 (mt) REVERT: G 572 ASP cc_start: 0.8418 (t0) cc_final: 0.8160 (t0) REVERT: G 644 LYS cc_start: 0.8631 (mtmp) cc_final: 0.8358 (mtmm) REVERT: C 403 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.7007 (tp) REVERT: C 585 ILE cc_start: 0.8738 (tt) cc_final: 0.8395 (mt) REVERT: B 2 ASP cc_start: 0.8184 (p0) cc_final: 0.7860 (p0) REVERT: B 189 ASP cc_start: 0.8520 (t0) cc_final: 0.8292 (t0) REVERT: I 83 LYS cc_start: 0.8647 (pttm) cc_final: 0.8417 (tmmt) REVERT: I 153 MET cc_start: 0.8872 (mmt) cc_final: 0.7980 (mmt) REVERT: L 407 MET cc_start: 0.7608 (tpt) cc_final: 0.6568 (tpt) REVERT: L 415 MET cc_start: 0.8000 (ttp) cc_final: 0.7677 (ttp) REVERT: M 235 MET cc_start: 0.8645 (ttp) cc_final: 0.8377 (ttm) REVERT: M 370 ASP cc_start: 0.8776 (t70) cc_final: 0.8542 (t0) REVERT: N 132 ILE cc_start: 0.8642 (pt) cc_final: 0.8357 (mt) REVERT: H 10 GLU cc_start: 0.8237 (tp30) cc_final: 0.8017 (tp30) REVERT: H 181 ASN cc_start: 0.8308 (m-40) cc_final: 0.8048 (m-40) REVERT: H 229 TYR cc_start: 0.9069 (m-80) cc_final: 0.8864 (m-80) REVERT: H 241 GLU cc_start: 0.7206 (tt0) cc_final: 0.6978 (tt0) REVERT: J 24 ASN cc_start: 0.8952 (p0) cc_final: 0.8720 (p0) REVERT: J 59 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8638 (t80) outliers start: 96 outliers final: 50 residues processed: 608 average time/residue: 0.2054 time to fit residues: 204.6767 Evaluate side-chains 570 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 517 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 93 ASP 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 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 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 47 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 522 VAL Chi-restraints excluded: chain B residue 95 LEU 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 105 CYS 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 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 259 LEU Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 128 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 H residue 100 ILE Chi-restraints excluded: chain H residue 157 GLU 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: 5.9990 chunk 91 optimal weight: 2.9990 chunk 436 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 110 HIS F 142 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 765 GLN ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 HIS H 214 GLN H 226 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.064674 restraints weight = 63040.299| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.31 r_work: 0.2747 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 37649 Z= 0.421 Angle : 2.536 50.751 51217 Z= 1.454 Chirality : 0.444 6.416 5753 Planarity : 0.005 0.102 6421 Dihedral : 6.075 174.419 5134 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.11 % Allowed : 14.91 % Favored : 81.97 % 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: 0.11 (0.12), residues: 4629 helix: 1.03 (0.10), residues: 2608 sheet: -0.56 (0.29), residues: 313 loop : -1.27 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 804 TYR 0.021 0.002 TYR M 435 PHE 0.039 0.002 PHE C 215 TRP 0.017 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01199 / 0.42 (37613) covalent geometry : angle 2.21149 / 1.45 (51124) hydrogen bonds : bond 0.04527 / 3.03 ( 1632) hydrogen bonds : angle 4.18016 / 2.92 ( 4896) metal coordination : bond 0.02774 / 1.80 ( 36) metal coordination : angle 29.22194 / 19.70 ( 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 652 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 533 time to evaluate : 1.210 Fit side-chains REVERT: F 309 MET cc_start: 0.9220 (mmm) cc_final: 0.8936 (mmm) REVERT: F 312 GLU cc_start: 0.8398 (pm20) cc_final: 0.8190 (pm20) REVERT: F 408 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.9021 (tp) REVERT: F 434 ASN cc_start: 0.8590 (t0) cc_final: 0.8169 (t0) REVERT: G 70 MET cc_start: 0.9031 (mmm) cc_final: 0.8799 (mmm) REVERT: G 485 ILE cc_start: 0.9272 (mm) cc_final: 0.9008 (mt) REVERT: G 644 LYS cc_start: 0.8618 (mtmp) cc_final: 0.8397 (mtmm) REVERT: G 670 GLN cc_start: 0.8743 (tt0) cc_final: 0.8395 (tt0) REVERT: C 344 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7959 (mm-40) REVERT: C 528 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7898 (mmt) REVERT: C 555 MET cc_start: 0.8945 (mtm) cc_final: 0.8723 (mtt) REVERT: C 585 ILE cc_start: 0.8732 (tt) cc_final: 0.8460 (mt) REVERT: B 2 ASP cc_start: 0.8249 (p0) cc_final: 0.8012 (p0) REVERT: B 126 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8851 (mmm) REVERT: I 153 MET cc_start: 0.8895 (mmt) cc_final: 0.7859 (mmt) REVERT: L 253 ILE cc_start: 0.8631 (tt) cc_final: 0.8330 (tt) REVERT: L 407 MET cc_start: 0.7760 (tpt) cc_final: 0.7222 (tpt) REVERT: L 415 MET cc_start: 0.8057 (ttp) cc_final: 0.7845 (ttp) REVERT: L 430 PHE cc_start: 0.8527 (m-80) cc_final: 0.8208 (m-80) REVERT: M 22 ARG cc_start: 0.6325 (OUTLIER) cc_final: 0.4185 (ptp-170) REVERT: M 145 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8766 (tmm) REVERT: M 235 MET cc_start: 0.8625 (ttp) cc_final: 0.8416 (ttm) REVERT: M 303 TRP cc_start: 0.8832 (OUTLIER) cc_final: 0.8317 (m-10) REVERT: M 370 ASP cc_start: 0.8833 (t70) cc_final: 0.8336 (t0) REVERT: N 81 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8762 (mm) REVERT: N 132 ILE cc_start: 0.8684 (pt) cc_final: 0.8472 (mt) REVERT: N 135 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8895 (mm) REVERT: H 10 GLU cc_start: 0.8206 (tp30) cc_final: 0.7990 (tp30) REVERT: H 147 MET cc_start: 0.8818 (mmm) cc_final: 0.8467 (mmp) REVERT: H 232 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8050 (tpp) REVERT: H 241 GLU cc_start: 0.7408 (tt0) cc_final: 0.7152 (tt0) REVERT: H 278 PHE cc_start: 0.8685 (m-80) cc_final: 0.8421 (m-80) REVERT: K 38 MET cc_start: 0.8833 (mtm) cc_final: 0.8491 (mtm) REVERT: J 59 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.8718 (t80) outliers start: 119 outliers final: 67 residues processed: 615 average time/residue: 0.2074 time to fit residues: 209.6832 Evaluate side-chains 568 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 491 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 408 LEU Chi-restraints excluded: chain F residue 430 THR 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 57 ASN Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 774 VAL Chi-restraints excluded: chain G residue 884 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 281 CYS Chi-restraints excluded: chain C residue 309 MET 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 C residue 580 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 126 MET 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 260 THR Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 392 VAL 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 259 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain H residue 284 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 34 ILE Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 93 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 258 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 309 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 195 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 457 optimal weight: 5.9990 chunk 387 optimal weight: 7.9990 chunk 370 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 ASN ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 ASN ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 ASN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN H 214 GLN H 226 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.077055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.063549 restraints weight = 62664.412| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.30 r_work: 0.2722 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 37649 Z= 0.429 Angle : 2.540 50.709 51217 Z= 1.455 Chirality : 0.444 6.416 5753 Planarity : 0.005 0.098 6421 Dihedral : 6.125 174.891 5134 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.66 % Allowed : 14.86 % Favored : 81.48 % 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: 0.18 (0.12), residues: 4629 helix: 1.07 (0.10), residues: 2598 sheet: -0.66 (0.29), residues: 317 loop : -1.18 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 804 TYR 0.020 0.002 TYR M 435 PHE 0.039 0.002 PHE C 215 TRP 0.015 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01215 / 0.43 (37613) covalent geometry : angle 2.21535 / 1.45 (51124) hydrogen bonds : bond 0.04649 / 3.12 ( 1632) hydrogen bonds : angle 4.22108 / 2.95 ( 4896) metal coordination : bond 0.02758 / 1.80 ( 36) metal coordination : angle 29.22647 / 19.73 ( 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 648 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 508 time to evaluate : 1.175 Fit side-chains REVERT: F 309 MET cc_start: 0.9249 (mmm) cc_final: 0.8969 (mmm) REVERT: F 434 ASN cc_start: 0.8671 (t0) cc_final: 0.8305 (t0) REVERT: G 293 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8876 (pt) REVERT: G 485 ILE cc_start: 0.9269 (mm) cc_final: 0.9002 (mt) REVERT: G 605 ASN cc_start: 0.8588 (p0) cc_final: 0.8226 (p0) REVERT: G 644 LYS cc_start: 0.8691 (mtmp) cc_final: 0.8459 (mtmm) REVERT: G 870 THR cc_start: 0.8907 (p) cc_final: 0.8680 (p) REVERT: C 275 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8600 (mm) REVERT: C 528 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7930 (mmt) REVERT: C 555 MET cc_start: 0.8974 (mtm) cc_final: 0.8706 (mtt) REVERT: C 585 ILE cc_start: 0.8712 (tt) cc_final: 0.8481 (mt) REVERT: B 2 ASP cc_start: 0.8343 (p0) cc_final: 0.8077 (p0) REVERT: I 153 MET cc_start: 0.8948 (mmt) cc_final: 0.7891 (mmt) REVERT: L 88 MET cc_start: 0.8866 (mmm) cc_final: 0.8326 (mmm) REVERT: L 253 ILE cc_start: 0.8666 (tt) cc_final: 0.8385 (tt) REVERT: L 407 MET cc_start: 0.7940 (tpt) cc_final: 0.7424 (tpt) REVERT: L 430 PHE cc_start: 0.8487 (m-80) cc_final: 0.8137 (m-80) REVERT: M 22 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.4353 (ptp-170) REVERT: M 145 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8800 (tmm) REVERT: M 303 TRP cc_start: 0.8892 (OUTLIER) cc_final: 0.8230 (m-10) REVERT: M 370 ASP cc_start: 0.8836 (t70) cc_final: 0.8345 (t0) REVERT: N 81 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8745 (mm) REVERT: N 139 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8681 (mt) REVERT: H 94 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8405 (mm) REVERT: H 220 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6609 (mm-30) REVERT: H 241 GLU cc_start: 0.7506 (tt0) cc_final: 0.7254 (tt0) REVERT: J 59 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.8722 (t80) outliers start: 140 outliers final: 89 residues processed: 605 average time/residue: 0.2037 time to fit residues: 202.4622 Evaluate side-chains 591 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 492 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 283 ASP Chi-restraints excluded: chain F residue 430 THR 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 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 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 860 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 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 275 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 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 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 200 MET 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 150 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 82 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 13 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 64 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 23 THR 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: 0.7980 chunk 116 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 217 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 chunk 384 optimal weight: 8.9990 chunk 213 optimal weight: 0.9990 chunk 390 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** C 544 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.064265 restraints weight = 62962.676| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.33 r_work: 0.2739 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2448 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= 0.404 Angle : 2.532 50.679 51217 Z= 1.452 Chirality : 0.443 6.394 5753 Planarity : 0.004 0.098 6421 Dihedral : 6.024 175.115 5134 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.98 % Allowed : 16.09 % Favored : 80.93 % 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: 0.28 (0.12), residues: 4629 helix: 1.18 (0.10), residues: 2602 sheet: -0.59 (0.29), residues: 315 loop : -1.19 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 804 TYR 0.022 0.001 TYR M 435 PHE 0.038 0.001 PHE C 215 TRP 0.017 0.001 TRP L 143 HIS 0.005 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01170 / 0.40 (37613) covalent geometry : angle 2.20544 / 1.45 (51124) hydrogen bonds : bond 0.04370 / 2.93 ( 1632) hydrogen bonds : angle 4.15375 / 2.90 ( 4896) metal coordination : bond 0.02346 / 1.54 ( 36) metal coordination : angle 29.27944 / 19.82 ( 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 629 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 515 time to evaluate : 1.059 Fit side-chains REVERT: F 277 TYR cc_start: 0.9379 (m-80) cc_final: 0.8416 (m-80) REVERT: F 285 LEU cc_start: 0.8652 (mt) cc_final: 0.8447 (mp) REVERT: F 434 ASN cc_start: 0.8590 (t0) cc_final: 0.8256 (t0) REVERT: G 98 MET cc_start: 0.8593 (mmm) cc_final: 0.8057 (mmm) REVERT: G 293 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8867 (pt) REVERT: G 485 ILE cc_start: 0.9232 (mm) cc_final: 0.8980 (mt) REVERT: G 605 ASN cc_start: 0.8612 (p0) cc_final: 0.8277 (p0) REVERT: G 644 LYS cc_start: 0.8676 (mtmp) cc_final: 0.8456 (mtmm) REVERT: G 670 GLN cc_start: 0.8746 (tt0) cc_final: 0.8403 (tt0) REVERT: G 870 THR cc_start: 0.8914 (p) cc_final: 0.8588 (p) REVERT: C 110 ASP cc_start: 0.8236 (p0) cc_final: 0.7985 (p0) REVERT: C 528 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7904 (mmt) REVERT: C 585 ILE cc_start: 0.8688 (tt) cc_final: 0.8458 (mt) REVERT: B 2 ASP cc_start: 0.8344 (p0) cc_final: 0.8027 (p0) REVERT: I 83 LYS cc_start: 0.8692 (ptpt) cc_final: 0.8453 (ptpt) REVERT: I 153 MET cc_start: 0.8980 (mmt) cc_final: 0.7932 (mmt) REVERT: L 88 MET cc_start: 0.8875 (mmm) cc_final: 0.8384 (mmm) REVERT: L 253 ILE cc_start: 0.8606 (tt) cc_final: 0.8288 (tt) REVERT: L 407 MET cc_start: 0.7789 (tpt) cc_final: 0.7201 (tpt) REVERT: L 415 MET cc_start: 0.8111 (ttp) cc_final: 0.7358 (ttp) REVERT: L 430 PHE cc_start: 0.8398 (m-80) cc_final: 0.8078 (m-80) REVERT: M 22 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.4375 (ptp-170) REVERT: M 145 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8793 (tmm) REVERT: M 303 TRP cc_start: 0.8889 (OUTLIER) cc_final: 0.8143 (m-10) REVERT: M 370 ASP cc_start: 0.8818 (t70) cc_final: 0.8323 (t0) REVERT: N 81 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8762 (mm) REVERT: N 139 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8673 (mt) REVERT: H 94 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8335 (mm) REVERT: H 147 MET cc_start: 0.8814 (mmm) cc_final: 0.8502 (mmp) REVERT: H 220 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6613 (mm-30) REVERT: H 241 GLU cc_start: 0.7501 (tt0) cc_final: 0.7215 (tt0) REVERT: H 278 PHE cc_start: 0.8619 (m-80) cc_final: 0.8378 (m-80) REVERT: J 59 TYR cc_start: 0.9244 (OUTLIER) cc_final: 0.8657 (t80) REVERT: J 80 GLU cc_start: 0.6927 (mp0) cc_final: 0.6641 (mp0) outliers start: 114 outliers final: 74 residues processed: 598 average time/residue: 0.2125 time to fit residues: 208.5314 Evaluate side-chains 577 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 494 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 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 131 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain G residue 57 ASN 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 453 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 559 GLU Chi-restraints excluded: chain G residue 631 ARG Chi-restraints excluded: chain G residue 774 VAL 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 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 138 ILE 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 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 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 M residue 303 TRP Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 81 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 410 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 94 LEU 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 64 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 404 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 332 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 435 optimal weight: 8.9990 chunk 380 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN 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 = 0.3086 r_free = 0.3086 target = 0.075965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.062693 restraints weight = 62340.390| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.22 r_work: 0.2704 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 37649 Z= 0.442 Angle : 2.549 50.721 51217 Z= 1.459 Chirality : 0.444 6.432 5753 Planarity : 0.005 0.099 6421 Dihedral : 6.160 174.940 5134 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.38 % Allowed : 16.14 % Favored : 80.48 % 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: 0.22 (0.12), residues: 4629 helix: 1.10 (0.10), residues: 2596 sheet: -0.69 (0.29), residues: 317 loop : -1.12 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 804 TYR 0.022 0.002 TYR C 277 PHE 0.052 0.002 PHE N 72 TRP 0.015 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01239 / 0.44 (37613) covalent geometry : angle 2.22412 / 1.46 (51124) hydrogen bonds : bond 0.04815 / 3.23 ( 1632) hydrogen bonds : angle 4.27726 / 2.99 ( 4896) metal coordination : bond 0.02886 / 1.92 ( 36) metal coordination : angle 29.28509 / 19.79 ( 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 625 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 496 time to evaluate : 1.177 Fit side-chains REVERT: F 220 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: F 277 TYR cc_start: 0.9404 (m-80) cc_final: 0.8355 (m-80) REVERT: F 285 LEU cc_start: 0.8728 (mt) cc_final: 0.8508 (mp) REVERT: F 387 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8585 (tp) REVERT: F 434 ASN cc_start: 0.8674 (t0) cc_final: 0.8407 (t0) REVERT: G 293 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8993 (pt) REVERT: G 485 ILE cc_start: 0.9262 (mm) cc_final: 0.9018 (mt) REVERT: G 605 ASN cc_start: 0.8656 (p0) cc_final: 0.8270 (p0) REVERT: G 644 LYS cc_start: 0.8716 (mtmp) cc_final: 0.8493 (mtmm) REVERT: G 670 GLN cc_start: 0.8785 (tt0) cc_final: 0.8440 (tt0) REVERT: G 811 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8628 (ttmm) REVERT: C 528 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7981 (mmt) REVERT: C 555 MET cc_start: 0.9002 (mtm) cc_final: 0.8793 (mtt) REVERT: C 585 ILE cc_start: 0.8699 (tt) cc_final: 0.8498 (mt) REVERT: B 2 ASP cc_start: 0.8316 (p0) cc_final: 0.7985 (p0) REVERT: I 153 MET cc_start: 0.9001 (mmt) cc_final: 0.7977 (mmt) REVERT: L 88 MET cc_start: 0.8834 (mmm) cc_final: 0.8340 (mmm) REVERT: L 407 MET cc_start: 0.7944 (tpt) cc_final: 0.7619 (tpt) REVERT: L 430 PHE cc_start: 0.8462 (m-80) cc_final: 0.8141 (m-80) REVERT: M 22 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.4501 (ptp-170) REVERT: M 145 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8818 (tmm) REVERT: M 303 TRP cc_start: 0.8929 (OUTLIER) cc_final: 0.8015 (m-10) REVERT: M 370 ASP cc_start: 0.8848 (t70) cc_final: 0.8366 (t0) REVERT: N 139 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8649 (mt) REVERT: N 324 GLU cc_start: 0.8520 (tt0) cc_final: 0.8317 (tt0) REVERT: H 94 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8486 (mm) REVERT: H 147 MET cc_start: 0.8836 (mmm) cc_final: 0.8415 (mmp) REVERT: H 220 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6776 (mm-30) REVERT: H 241 GLU cc_start: 0.7534 (tt0) cc_final: 0.7277 (tt0) REVERT: H 278 PHE cc_start: 0.8708 (m-80) cc_final: 0.8377 (m-80) REVERT: J 59 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.8737 (t80) REVERT: J 80 GLU cc_start: 0.7101 (mp0) cc_final: 0.6791 (mp0) outliers start: 129 outliers final: 90 residues processed: 590 average time/residue: 0.2102 time to fit residues: 203.1149 Evaluate side-chains 578 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 477 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 229 LEU 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 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 385 THR 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 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 100 TYR 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 138 ILE Chi-restraints excluded: chain B residue 158 CYS 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 91 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 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 L residue 500 VAL 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 237 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 303 TRP 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 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 74 ILE 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 232 MET 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 92 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 277 optimal weight: 0.3980 chunk 411 optimal weight: 6.9990 chunk 414 optimal weight: 0.5980 chunk 296 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 385 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 263 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 307 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.079030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.065675 restraints weight = 62181.890| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.27 r_work: 0.2772 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 37649 Z= 0.392 Angle : 2.530 50.677 51217 Z= 1.450 Chirality : 0.441 6.371 5753 Planarity : 0.004 0.095 6421 Dihedral : 5.924 175.053 5134 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.64 % Allowed : 17.09 % Favored : 80.27 % 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: 2610 sheet: -0.61 (0.29), residues: 320 loop : -1.10 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 87 TYR 0.025 0.001 TYR M 435 PHE 0.045 0.001 PHE N 72 TRP 0.018 0.001 TRP L 143 HIS 0.004 0.001 HIS L 334 Details of bonding type rmsd/Z covalent geometry : bond 0.01150 / 0.39 (37613) covalent geometry : angle 2.20152 / 1.45 (51124) hydrogen bonds : bond 0.04143 / 2.78 ( 1632) hydrogen bonds : angle 4.09743 / 2.86 ( 4896) metal coordination : bond 0.01983 / 1.31 ( 36) metal coordination : angle 29.33518 / 19.89 ( 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 616 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 515 time to evaluate : 1.363 Fit side-chains REVERT: F 277 TYR cc_start: 0.9367 (m-80) cc_final: 0.8536 (m-80) REVERT: F 285 LEU cc_start: 0.8605 (mt) cc_final: 0.8324 (mp) REVERT: F 387 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8531 (tp) REVERT: F 434 ASN cc_start: 0.8527 (t0) cc_final: 0.8281 (t0) REVERT: G 293 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8921 (pt) REVERT: G 485 ILE cc_start: 0.9213 (mm) cc_final: 0.8952 (mt) REVERT: G 605 ASN cc_start: 0.8591 (p0) cc_final: 0.8259 (p0) REVERT: G 644 LYS cc_start: 0.8665 (mtmp) cc_final: 0.8452 (mtmm) REVERT: G 670 GLN cc_start: 0.8733 (tt0) cc_final: 0.8412 (tt0) REVERT: C 528 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7751 (mmt) REVERT: C 555 MET cc_start: 0.9000 (mtm) cc_final: 0.8760 (mtt) REVERT: C 585 ILE cc_start: 0.8658 (tt) cc_final: 0.8433 (mt) REVERT: B 2 ASP cc_start: 0.8311 (p0) cc_final: 0.8011 (p0) REVERT: B 106 MET cc_start: 0.8629 (mmm) cc_final: 0.8396 (tpp) REVERT: I 83 LYS cc_start: 0.8658 (ptpt) cc_final: 0.8451 (ptpt) REVERT: I 153 MET cc_start: 0.8995 (mmt) cc_final: 0.8148 (mmt) REVERT: L 253 ILE cc_start: 0.8529 (tt) cc_final: 0.8275 (tt) REVERT: L 326 GLN cc_start: 0.8928 (mp10) cc_final: 0.8544 (mp10) REVERT: L 415 MET cc_start: 0.8074 (ttp) cc_final: 0.7235 (ttp) REVERT: L 430 PHE cc_start: 0.8276 (m-80) cc_final: 0.8014 (m-80) REVERT: M 145 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8826 (tmm) REVERT: M 303 TRP cc_start: 0.8904 (OUTLIER) cc_final: 0.8090 (m-10) REVERT: M 370 ASP cc_start: 0.8851 (t70) cc_final: 0.8628 (t0) REVERT: N 139 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8617 (mm) REVERT: N 223 PHE cc_start: 0.9498 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: H 94 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8217 (mm) REVERT: H 220 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6750 (mm-30) REVERT: H 241 GLU cc_start: 0.7531 (tt0) cc_final: 0.7289 (tt0) REVERT: H 278 PHE cc_start: 0.8624 (m-80) cc_final: 0.8338 (m-80) REVERT: K 32 LEU cc_start: 0.8804 (mt) cc_final: 0.8487 (mt) REVERT: J 59 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.8648 (t80) REVERT: J 80 GLU cc_start: 0.7087 (mp0) cc_final: 0.6771 (mp0) outliers start: 101 outliers final: 69 residues processed: 586 average time/residue: 0.2265 time to fit residues: 217.5437 Evaluate side-chains 570 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 492 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 LEU Chi-restraints excluded: chain F residue 387 LEU 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 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 181 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 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 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 C residue 528 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain I residue 66 CYS 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 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 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 M residue 303 TRP 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 388 MET Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 74 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 165 optimal weight: 10.0000 chunk 345 optimal weight: 1.9990 chunk 147 optimal weight: 0.0060 chunk 181 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 315 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 386 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** H 181 ASN H 214 GLN H 219 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 = 0.3116 r_free = 0.3116 target = 0.077580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.064099 restraints weight = 62229.746| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.26 r_work: 0.2737 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2722 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= 0.409 Angle : 2.536 50.693 51217 Z= 1.453 Chirality : 0.443 6.397 5753 Planarity : 0.004 0.093 6421 Dihedral : 5.948 175.074 5134 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.62 % Allowed : 17.50 % Favored : 79.88 % 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: 0.42 (0.12), residues: 4629 helix: 1.27 (0.10), residues: 2599 sheet: -0.58 (0.29), residues: 312 loop : -1.08 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 87 TYR 0.027 0.002 TYR C 277 PHE 0.050 0.002 PHE N 72 TRP 0.017 0.001 TRP L 143 HIS 0.006 0.001 HIS M 80 Details of bonding type rmsd/Z covalent geometry : bond 0.01180 / 0.41 (37613) covalent geometry : angle 2.21070 / 1.45 (51124) hydrogen bonds : bond 0.04389 / 2.95 ( 1632) hydrogen bonds : angle 4.14932 / 2.90 ( 4896) metal coordination : bond 0.02475 / 1.65 ( 36) metal coordination : angle 29.26168 / 19.80 ( 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 594 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 494 time to evaluate : 1.409 Fit side-chains REVERT: F 220 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: F 285 LEU cc_start: 0.8628 (mt) cc_final: 0.8355 (mp) REVERT: F 387 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8538 (tp) REVERT: F 434 ASN cc_start: 0.8691 (t0) cc_final: 0.8448 (t0) REVERT: G 288 ARG cc_start: 0.7864 (ptp90) cc_final: 0.7554 (ptp90) REVERT: G 380 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8798 (mt) REVERT: G 485 ILE cc_start: 0.9234 (mm) cc_final: 0.8977 (mt) REVERT: G 605 ASN cc_start: 0.8631 (p0) cc_final: 0.8282 (p0) REVERT: G 644 LYS cc_start: 0.8713 (mtmp) cc_final: 0.8485 (mtmm) REVERT: G 670 GLN cc_start: 0.8778 (tt0) cc_final: 0.8406 (tt0) REVERT: C 528 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7798 (mmt) REVERT: C 585 ILE cc_start: 0.8701 (tt) cc_final: 0.8483 (mt) REVERT: B 2 ASP cc_start: 0.8319 (p0) cc_final: 0.7989 (p0) REVERT: I 83 LYS cc_start: 0.8678 (ptpt) cc_final: 0.8475 (ptpt) REVERT: I 153 MET cc_start: 0.8990 (mmt) cc_final: 0.8138 (mmt) REVERT: L 88 MET cc_start: 0.8827 (mmm) cc_final: 0.8436 (mmm) REVERT: L 253 ILE cc_start: 0.8554 (tt) cc_final: 0.8297 (tt) REVERT: L 326 GLN cc_start: 0.8963 (mp10) cc_final: 0.8555 (mp10) REVERT: L 430 PHE cc_start: 0.8332 (m-80) cc_final: 0.8093 (m-80) REVERT: M 22 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.4399 (ptp-170) REVERT: M 121 MET cc_start: 0.8923 (mmp) cc_final: 0.8689 (mmm) REVERT: M 136 MET cc_start: 0.8775 (mmm) cc_final: 0.8425 (mmp) REVERT: M 145 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8832 (tmm) REVERT: M 303 TRP cc_start: 0.8913 (OUTLIER) cc_final: 0.8118 (m-10) REVERT: M 364 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8346 (tm-30) REVERT: M 370 ASP cc_start: 0.8863 (t70) cc_final: 0.8646 (t0) REVERT: N 139 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8649 (mt) REVERT: N 223 PHE cc_start: 0.9506 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: H 94 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8283 (mm) REVERT: H 147 MET cc_start: 0.8779 (mmm) cc_final: 0.8474 (mmp) REVERT: H 220 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6827 (mm-30) REVERT: J 59 TYR cc_start: 0.9226 (OUTLIER) cc_final: 0.8611 (t80) REVERT: J 80 GLU cc_start: 0.7142 (mp0) cc_final: 0.6791 (mp0) outliers start: 100 outliers final: 78 residues processed: 567 average time/residue: 0.2182 time to fit residues: 202.8920 Evaluate side-chains 570 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 481 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 LEU 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 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 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 380 LEU 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 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 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 C residue 528 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain I residue 66 CYS 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 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 500 VAL 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 174 PHE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 396 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 N residue 432 LEU Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 92 ILE 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: 0.9990 chunk 208 optimal weight: 20.0000 chunk 324 optimal weight: 0.9990 chunk 232 optimal weight: 6.9990 chunk 359 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 chunk 454 optimal weight: 8.9990 chunk 314 optimal weight: 0.0030 chunk 383 optimal weight: 6.9990 chunk 306 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 162 GLN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 ASN H 214 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 = 0.3155 r_free = 0.3155 target = 0.079621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.066436 restraints weight = 62331.103| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.28 r_work: 0.2782 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.247 37649 Z= 0.391 Angle : 2.530 50.667 51217 Z= 1.450 Chirality : 0.441 6.367 5753 Planarity : 0.004 0.091 6421 Dihedral : 5.819 174.814 5134 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.15 % Allowed : 18.03 % Favored : 79.83 % 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: 0.52 (0.12), residues: 4629 helix: 1.35 (0.10), residues: 2609 sheet: -0.52 (0.29), residues: 317 loop : -1.04 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 859 TYR 0.024 0.001 TYR M 435 PHE 0.047 0.001 PHE N 72 TRP 0.018 0.001 TRP L 143 HIS 0.004 0.001 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.01149 / 0.39 (37613) covalent geometry : angle 2.20148 / 1.45 (51124) hydrogen bonds : bond 0.04027 / 2.70 ( 1632) hydrogen bonds : angle 4.05862 / 2.84 ( 4896) metal coordination : bond 0.01927 / 1.28 ( 36) metal coordination : angle 29.32831 / 19.89 ( 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 592 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 510 time to evaluate : 1.256 Fit side-chains REVERT: F 277 TYR cc_start: 0.9365 (m-80) cc_final: 0.8484 (m-80) REVERT: F 285 LEU cc_start: 0.8584 (mt) cc_final: 0.8298 (mp) REVERT: F 387 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8501 (tp) REVERT: F 434 ASN cc_start: 0.8506 (t0) cc_final: 0.8268 (t0) REVERT: G 485 ILE cc_start: 0.9225 (mm) cc_final: 0.8961 (mt) REVERT: G 644 LYS cc_start: 0.8625 (mtmp) cc_final: 0.8417 (mtmm) REVERT: G 670 GLN cc_start: 0.8702 (tt0) cc_final: 0.8406 (tt0) REVERT: C 528 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7614 (mtt) REVERT: C 585 ILE cc_start: 0.8715 (tt) cc_final: 0.8476 (mt) REVERT: B 2 ASP cc_start: 0.8329 (p0) cc_final: 0.7968 (p0) REVERT: B 67 GLU cc_start: 0.8414 (tp30) cc_final: 0.8043 (tp30) REVERT: B 106 MET cc_start: 0.8642 (mmm) cc_final: 0.8429 (tpp) REVERT: I 153 MET cc_start: 0.8995 (mmt) cc_final: 0.8218 (mmt) REVERT: L 88 MET cc_start: 0.8892 (mmm) cc_final: 0.8459 (mmm) REVERT: L 253 ILE cc_start: 0.8547 (tt) cc_final: 0.8281 (tt) REVERT: L 326 GLN cc_start: 0.8946 (mp10) cc_final: 0.8458 (mp10) REVERT: M 121 MET cc_start: 0.8900 (mmp) cc_final: 0.8671 (mmm) REVERT: M 145 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8811 (tmm) REVERT: M 303 TRP cc_start: 0.8888 (OUTLIER) cc_final: 0.8173 (m-10) REVERT: M 370 ASP cc_start: 0.8838 (t70) cc_final: 0.8636 (t0) REVERT: N 139 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8641 (mm) REVERT: N 223 PHE cc_start: 0.9502 (OUTLIER) cc_final: 0.7580 (m-80) REVERT: H 94 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8049 (mm) REVERT: H 147 MET cc_start: 0.8705 (mmm) cc_final: 0.8415 (mmp) REVERT: H 220 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6808 (mm-30) REVERT: H 278 PHE cc_start: 0.8586 (m-80) cc_final: 0.8262 (m-80) REVERT: J 80 GLU cc_start: 0.7144 (mp0) cc_final: 0.6807 (mp0) outliers start: 82 outliers final: 67 residues processed: 569 average time/residue: 0.2150 time to fit residues: 202.1257 Evaluate side-chains 560 residues out of total 3830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 486 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 LEU 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 131 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 105 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 237 CYS Chi-restraints excluded: chain G residue 259 VAL 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 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 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 C residue 528 MET Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain I residue 66 CYS 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 372 ILE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 38 LEU 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 M residue 303 TRP Chi-restraints excluded: chain M residue 396 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 N residue 482 MET Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain A residue 10 ILE 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 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: 4.9990 chunk 246 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 443 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 258 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 307 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 B 47 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 ASN H 226 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.079617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.066616 restraints weight = 62104.916| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.22 r_work: 0.2789 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 37649 Z= 0.392 Angle : 2.530 50.660 51217 Z= 1.450 Chirality : 0.442 6.370 5753 Planarity : 0.004 0.091 6421 Dihedral : 5.766 174.451 5134 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.15 % Allowed : 18.18 % Favored : 79.67 % 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: 0.57 (0.13), residues: 4629 helix: 1.39 (0.10), residues: 2603 sheet: -0.50 (0.30), residues: 303 loop : -1.01 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 859 TYR 0.024 0.001 TYR M 435 PHE 0.029 0.001 PHE C 215 TRP 0.019 0.001 TRP N 53 HIS 0.004 0.001 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.01150 / 0.39 (37613) covalent geometry : angle 2.20290 / 1.45 (51124) hydrogen bonds : bond 0.04051 / 2.74 ( 1632) hydrogen bonds : angle 4.04291 / 2.83 ( 4896) metal coordination : bond 0.02038 / 1.36 ( 36) metal coordination : angle 29.26850 / 19.85 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10413.83 seconds wall clock time: 178 minutes 29.64 seconds (10709.64 seconds total)