Starting phenix.real_space_refine on Sat Feb 7 22:16:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z80_14540/02_2026/7z80_14540.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z80_14540/02_2026/7z80_14540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z80_14540/02_2026/7z80_14540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z80_14540/02_2026/7z80_14540.map" model { file = "/net/cci-nas-00/data/ceres_data/7z80_14540/02_2026/7z80_14540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z80_14540/02_2026/7z80_14540.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.018 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 13 5.49 5 S 267 5.16 5 C 24601 2.51 5 N 6260 2.21 5 O 6647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37821 Number of models: 1 Model: "" Number of chains: 24 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7012 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 41, 'TRANS': 863} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4762 Classifications: {'peptide': 589} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 551} Chain: "B" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1693 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2534 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Chain: "A" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "L" Number of atoms: 4560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4560 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 579} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3542 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 447} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 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: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'3PE': 1, 'DCQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'DCQ': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 198 Unusual residues: {'3PE': 4, 'LFA': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "M" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 72.862 61.412 190.359 1.00 20.38 S ATOM 2741 SG CYS F 357 76.312 61.121 194.922 1.00 24.36 S ATOM 3062 SG CYS F 398 70.502 57.796 195.348 1.00 32.12 S ATOM 2697 SG CYS F 351 75.092 55.202 191.892 1.00 15.35 S ATOM 4054 SG CYS E 92 82.919 53.754 211.869 1.00 29.89 S ATOM 4088 SG CYS E 97 82.964 54.641 215.396 1.00 51.52 S ATOM 4366 SG CYS E 133 77.760 53.013 211.500 1.00 31.00 S ATOM 4392 SG CYS E 137 76.906 53.913 214.716 1.00 58.96 S ATOM 5472 SG CYS G 114 83.716 67.139 173.080 1.00 11.04 S ATOM 5412 SG CYS G 105 88.807 71.031 174.765 1.00 11.14 S ATOM 5432 SG CYS G 108 89.682 64.966 172.639 1.00 35.81 S ATOM 5826 SG CYS G 156 77.823 59.574 178.079 1.00 30.27 S ATOM 5807 SG CYS G 153 83.584 58.564 181.225 1.00 23.88 S ATOM 5855 SG CYS G 159 80.880 53.861 177.696 1.00 15.75 S ATOM 6199 SG CYS G 203 82.996 59.004 174.552 1.00 8.59 S ATOM 6424 SG CYS G 230 80.320 50.034 153.518 1.00 27.35 S ATOM 6709 SG CYS G 265 80.101 46.367 158.884 1.00 4.73 S ATOM 6472 SG CYS G 237 74.838 49.704 156.464 1.00 19.09 S ATOM 6448 SG CYS G 233 77.190 44.274 153.595 1.00 19.61 S ATOM 4877 SG CYS G 36 71.357 60.511 180.475 1.00 12.86 S ATOM 4953 SG CYS G 47 72.931 63.881 180.891 1.00 25.01 S ATOM 4979 SG CYS G 50 67.164 65.551 180.853 1.00 23.27 S ATOM 5124 SG CYS G 69 66.661 61.930 180.443 1.00 22.68 S ATOM 17372 SG CYS B 129 94.338 93.908 149.046 1.00 28.74 S ATOM 16869 SG CYS B 64 99.530 97.769 150.534 1.00 16.12 S ATOM 16863 SG CYS B 63 93.940 99.863 152.287 1.00 17.62 S ATOM 17589 SG CYS B 158 96.105 94.149 154.850 1.00 34.45 S ATOM 18920 SG CYS I 102 94.647 88.411 161.060 1.00 13.41 S ATOM 18895 SG CYS I 99 100.055 87.017 157.367 1.00 16.26 S ATOM 18938 SG CYS I 105 98.705 83.823 162.891 1.00 20.19 S ATOM 18653 SG CYS I 70 94.831 83.008 157.729 1.00 30.78 S ATOM 18967 SG CYS I 109 99.568 78.439 169.233 1.00 28.47 S ATOM 18630 SG CYS I 66 97.626 77.521 163.098 1.00 9.33 S ATOM 18590 SG CYS I 60 101.638 73.252 165.690 1.00 31.72 S ATOM 18608 SG CYS I 63 95.359 73.845 167.919 1.00 15.75 S Time building chain proxies: 7.89, per 1000 atoms: 0.21 Number of scatterers: 37821 At special positions: 0 Unit cell: (159, 219.42, 241.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 267 16.00 P 13 15.00 O 6647 8.00 N 6260 7.00 C 24601 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: 3.46 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="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 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8704 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 0 sheets defined 51.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 271 through 274 No H-bonds generated for 'chain 'F' and resid 271 through 274' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 419 No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 35 through 47 Processing helix chain 'E' and resid 53 through 62 Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 98 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.823A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 273 through 276 No H-bonds generated for 'chain 'G' and resid 273 through 276' Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.373A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 764 through 770 removed outlier: 5.179A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS G 769 " --> pdb=" O GLN G 765 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE G 770 " --> pdb=" O ALA G 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 770' Processing helix chain 'G' and resid 825 through 829 removed outlier: 4.374A pdb=" N ARG G 829 " --> pdb=" O GLU G 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 825 through 829' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 66 removed outlier: 5.193A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 5.692A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.151A pdb=" N PHE C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 399 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 575 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.706A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'H' and resid 6 through 44 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.947A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU H 95 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 4.594A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.555A pdb=" N VAL H 158 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU H 164 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 322 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 68 through 89 removed outlier: 4.069A pdb=" N ILE A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'L' and resid 4 through 21 removed outlier: 4.390A pdb=" N ILE L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 237 through 244 removed outlier: 5.387A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 259 through 268 removed outlier: 4.530A pdb=" N VAL L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 275 Processing helix chain 'L' and resid 277 through 299 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 519 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 548 Processing helix chain 'L' and resid 550 through 562 removed outlier: 4.995A pdb=" N ARG L 562 " --> pdb=" O TRP L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 584 Proline residue: L 572 - end of helix Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 28 through 50 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 157 removed outlier: 4.473A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 200 Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 removed outlier: 4.077A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 491 through 502 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.313A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.147A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.344A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 3.947A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 56 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'J' and resid 90 through 112 Proline residue: J 96 - end of helix removed outlier: 4.246A pdb=" N LEU J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1700 hydrogen bonds defined for protein. 5100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.07 Time building geometry restraints manager: 4.41 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: 16091 1.42 - 1.64: 22170 1.64 - 1.86: 409 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 38762 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.385 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.374 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.607 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C10 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.443 1.384 0.059 2.00e-02 2.50e+03 8.79e+00 bond pdb=" O13 3PE J 202 " pdb=" P 3PE J 202 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.68e+00 ... (remaining 38757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 52028 3.11 - 6.22: 438 6.22 - 9.33: 89 9.33 - 12.44: 15 12.44 - 15.54: 7 Bond angle restraints: 52577 Sorted by residual: angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.43 12.38 2.21e+00 2.05e-01 3.14e+01 angle pdb=" CB MET M 136 " pdb=" CG MET M 136 " pdb=" SD MET M 136 " ideal model delta sigma weight residual 112.70 126.97 -14.27 3.00e+00 1.11e-01 2.26e+01 angle pdb=" CA TYR J 109 " pdb=" CB TYR J 109 " pdb=" CG TYR J 109 " ideal model delta sigma weight residual 113.90 122.26 -8.36 1.80e+00 3.09e-01 2.16e+01 angle pdb=" C ALA G 177 " pdb=" N HIS G 178 " pdb=" CA HIS G 178 " ideal model delta sigma weight residual 121.19 128.56 -7.37 1.59e+00 3.96e-01 2.15e+01 angle pdb=" C GLN C 571 " pdb=" N ILE C 572 " pdb=" CA ILE C 572 " ideal model delta sigma weight residual 120.43 124.80 -4.37 9.60e-01 1.09e+00 2.07e+01 ... (remaining 52572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.33: 20931 23.33 - 46.67: 1618 46.67 - 70.00: 274 70.00 - 93.33: 51 93.33 - 116.66: 5 Dihedral angle restraints: 22879 sinusoidal: 9269 harmonic: 13610 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 133.62 46.38 0 5.00e+00 4.00e-02 8.60e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 144.35 35.65 0 5.00e+00 4.00e-02 5.08e+01 dihedral pdb=" CA ILE E 145 " pdb=" C ILE E 145 " pdb=" N ASP E 146 " pdb=" CA ASP E 146 " ideal model delta harmonic sigma weight residual -180.00 -153.73 -26.27 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 22876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.234: 5825 4.234 - 8.469: 0 8.469 - 12.703: 0 12.703 - 16.937: 0 16.937 - 21.171: 28 Chirality restraints: 5853 Sorted by residual: chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " 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="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.17 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5850 not shown) Planarity restraints: 6572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ H 602 " 0.060 2.00e-02 2.50e+03 1.19e-01 4.26e+02 pdb=" C1M DCQ H 602 " 0.269 2.00e-02 2.50e+03 pdb=" C2 DCQ H 602 " -0.034 2.00e-02 2.50e+03 pdb=" C3 DCQ H 602 " -0.020 2.00e-02 2.50e+03 pdb=" C4 DCQ H 602 " 0.026 2.00e-02 2.50e+03 pdb=" C5 DCQ H 602 " -0.028 2.00e-02 2.50e+03 pdb=" C6 DCQ H 602 " -0.079 2.00e-02 2.50e+03 pdb=" C7 DCQ H 602 " -0.148 2.00e-02 2.50e+03 pdb=" O2 DCQ H 602 " -0.130 2.00e-02 2.50e+03 pdb=" O3 DCQ H 602 " -0.083 2.00e-02 2.50e+03 pdb=" O4 DCQ H 602 " 0.196 2.00e-02 2.50e+03 pdb=" O5 DCQ H 602 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DCQ C 702 " 0.026 2.00e-02 2.50e+03 5.50e-02 9.07e+01 pdb=" C1M DCQ C 702 " 0.052 2.00e-02 2.50e+03 pdb=" C2 DCQ C 702 " 0.018 2.00e-02 2.50e+03 pdb=" C3 DCQ C 702 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DCQ C 702 " 0.032 2.00e-02 2.50e+03 pdb=" C5 DCQ C 702 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DCQ C 702 " -0.021 2.00e-02 2.50e+03 pdb=" C7 DCQ C 702 " -0.083 2.00e-02 2.50e+03 pdb=" O2 DCQ C 702 " 0.019 2.00e-02 2.50e+03 pdb=" O3 DCQ C 702 " -0.131 2.00e-02 2.50e+03 pdb=" O4 DCQ C 702 " 0.080 2.00e-02 2.50e+03 pdb=" O5 DCQ C 702 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C VAL N 63 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.024 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.020 2.00e-02 2.50e+03 ... (remaining 6569 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3541 2.75 - 3.29: 37130 3.29 - 3.82: 69507 3.82 - 4.36: 83781 4.36 - 4.90: 141875 Nonbonded interactions: 335834 Sorted by model distance: nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.210 3.040 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR I 82 " pdb=" OD1 ASP I 84 " model vdw 2.233 3.040 nonbonded pdb=" OG SER B 199 " pdb=" OE1 GLU B 202 " model vdw 2.244 3.040 nonbonded pdb=" OG SER C 226 " pdb=" O GLN H 219 " model vdw 2.252 3.040 ... (remaining 335829 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: 0.520 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: 0.810 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 39.020 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:9.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.167 38798 Z= 0.219 Angle : 0.808 15.544 52670 Z= 0.398 Chirality : 1.462 21.171 5853 Planarity : 0.006 0.119 6572 Dihedral : 16.602 116.662 14175 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.43 % Favored : 97.55 % Rotamer: Outliers : 2.08 % Allowed : 20.21 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.11), residues: 4728 helix: 0.26 (0.09), residues: 2653 sheet: -0.64 (0.28), residues: 326 loop : -1.08 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 804 TYR 0.036 0.002 TYR M 197 PHE 0.038 0.002 PHE L 341 TRP 0.016 0.001 TRP G 653 HIS 0.005 0.001 HIS L 254 Details of bonding type rmsd covalent geometry : bond 0.00462 (38762) covalent geometry : angle 0.79435 (52577) hydrogen bonds : bond 0.05019 ( 1700) hydrogen bonds : angle 4.61783 ( 5100) metal coordination : bond 0.05852 ( 36) metal coordination : angle 3.56626 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 486 time to evaluate : 1.648 Fit side-chains REVERT: G 301 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8414 (mmt) REVERT: C 216 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7696 (tmm) REVERT: C 228 HIS cc_start: 0.7179 (m90) cc_final: 0.6967 (m170) REVERT: H 232 MET cc_start: 0.8484 (mmm) cc_final: 0.8278 (mmp) REVERT: M 224 MET cc_start: 0.8633 (tmm) cc_final: 0.8401 (tmm) REVERT: K 99 ARG cc_start: 0.7886 (ptp90) cc_final: 0.7682 (ptp-110) outliers start: 81 outliers final: 56 residues processed: 548 average time/residue: 0.7163 time to fit residues: 475.9589 Evaluate side-chains 511 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 453 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain G residue 301 MET Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 650 SER Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 412 ILE Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 369 ARG Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 70 ASP Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 345 SER Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 422 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 79 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.2980 chunk 401 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 159 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 513 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 670 GLN ** G 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN C 101 HIS C 344 GLN H 152 GLN L 301 GLN M 322 HIS M 335 GLN M 348 HIS M 441 HIS M 502 ASN K 40 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.087930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.070954 restraints weight = 55401.366| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.21 r_work: 0.2870 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.267 38798 Z= 0.389 Angle : 2.482 52.517 52670 Z= 1.426 Chirality : 0.446 6.525 5853 Planarity : 0.004 0.054 6572 Dihedral : 9.525 111.415 5820 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.21 % Allowed : 17.69 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 4728 helix: 0.96 (0.10), residues: 2670 sheet: -0.44 (0.28), residues: 325 loop : -0.85 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 30 TYR 0.022 0.002 TYR L 428 PHE 0.027 0.001 PHE L 341 TRP 0.018 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01120 (38762) covalent geometry : angle 2.16609 (52577) hydrogen bonds : bond 0.04695 ( 1700) hydrogen bonds : angle 4.15826 ( 5100) metal coordination : bond 0.04873 ( 36) metal coordination : angle 28.92396 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 473 time to evaluate : 1.406 Fit side-chains REVERT: F 48 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8349 (t0) REVERT: G 332 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6493 (tm-30) REVERT: G 496 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8225 (mptp) REVERT: C 482 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: I 126 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8649 (mttm) REVERT: H 228 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8428 (mp0) REVERT: H 242 TYR cc_start: 0.8724 (m-80) cc_final: 0.8332 (m-80) REVERT: L 430 PHE cc_start: 0.7878 (m-10) cc_final: 0.7667 (m-80) REVERT: M 185 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.9082 (ttm) REVERT: M 304 MET cc_start: 0.8650 (mmm) cc_final: 0.8187 (mmp) REVERT: M 372 ARG cc_start: 0.8003 (mtm180) cc_final: 0.7516 (mtm180) REVERT: N 255 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7791 (mtm) REVERT: K 1 MET cc_start: 0.7648 (tmm) cc_final: 0.6791 (tmm) REVERT: K 87 ARG cc_start: 0.7813 (tmt90) cc_final: 0.7566 (tmt90) REVERT: J 1 MET cc_start: 0.7988 (ttm) cc_final: 0.7663 (ttm) outliers start: 125 outliers final: 51 residues processed: 545 average time/residue: 0.6866 time to fit residues: 452.2102 Evaluate side-chains 511 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 452 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 434 optimal weight: 8.9990 chunk 111 optimal weight: 0.0060 chunk 91 optimal weight: 8.9990 chunk 439 optimal weight: 6.9990 chunk 398 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 338 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 250 optimal weight: 0.0470 overall best weight: 3.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 159 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 670 GLN ** G 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 301 GLN M 335 GLN M 502 ASN N 291 GLN K 40 ASN J 83 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.086401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.069392 restraints weight = 55261.874| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.19 r_work: 0.2835 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 38798 Z= 0.401 Angle : 2.484 53.024 52670 Z= 1.428 Chirality : 0.443 6.498 5853 Planarity : 0.004 0.055 6572 Dihedral : 9.030 108.569 5763 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.34 % Allowed : 18.05 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.12), residues: 4728 helix: 1.17 (0.10), residues: 2681 sheet: -0.38 (0.29), residues: 311 loop : -0.68 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 30 TYR 0.021 0.002 TYR N 424 PHE 0.027 0.002 PHE L 341 TRP 0.018 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01151 (38762) covalent geometry : angle 2.16857 (52577) hydrogen bonds : bond 0.04890 ( 1700) hydrogen bonds : angle 4.14176 ( 5100) metal coordination : bond 0.04073 ( 36) metal coordination : angle 28.90268 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 467 time to evaluate : 1.486 Fit side-chains REVERT: F 255 ARG cc_start: 0.8857 (mtt-85) cc_final: 0.8536 (mtt-85) REVERT: E 47 ARG cc_start: 0.8870 (mtt90) cc_final: 0.8488 (mtt90) REVERT: G 56 GLN cc_start: 0.7189 (pt0) cc_final: 0.6858 (mm-40) REVERT: G 332 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: G 496 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8517 (mptp) REVERT: C 448 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8787 (pm20) REVERT: C 482 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: C 597 ASP cc_start: 0.8711 (t0) cc_final: 0.8223 (t0) REVERT: B 13 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: B 57 TYR cc_start: 0.8854 (t80) cc_final: 0.8536 (t80) REVERT: I 126 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8656 (mttm) REVERT: H 36 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: H 228 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: H 242 TYR cc_start: 0.8789 (m-80) cc_final: 0.8377 (m-80) REVERT: A 79 ASP cc_start: 0.8354 (t0) cc_final: 0.8090 (t0) REVERT: L 127 MET cc_start: 0.8502 (tpt) cc_final: 0.8204 (tpt) REVERT: L 430 PHE cc_start: 0.7873 (m-10) cc_final: 0.7668 (m-80) REVERT: L 571 ILE cc_start: 0.7603 (mt) cc_final: 0.7247 (mp) REVERT: M 74 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7357 (tpt170) REVERT: M 185 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.9082 (ttm) REVERT: M 382 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7846 (mmtt) REVERT: M 398 MET cc_start: 0.8763 (tpt) cc_final: 0.8451 (tpt) REVERT: N 255 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7746 (mtm) REVERT: K 87 ARG cc_start: 0.7867 (tmt90) cc_final: 0.7620 (tmt90) REVERT: J 55 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: J 91 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7881 (pp30) REVERT: J 109 TYR cc_start: 0.8435 (t80) cc_final: 0.8137 (t80) outliers start: 130 outliers final: 60 residues processed: 543 average time/residue: 0.6961 time to fit residues: 456.6462 Evaluate side-chains 531 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 457 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 382 LYS Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 117 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 441 optimal weight: 5.9990 chunk 435 optimal weight: 3.9990 chunk 363 optimal weight: 3.9990 chunk 266 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 423 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 159 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN A 47 ASN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 495 ASN M 502 ASN K 40 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.084685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.067595 restraints weight = 54847.201| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.18 r_work: 0.2796 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 38798 Z= 0.423 Angle : 2.493 51.085 52670 Z= 1.432 Chirality : 0.444 6.510 5853 Planarity : 0.005 0.060 6572 Dihedral : 9.169 101.580 5756 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.66 % Favored : 97.31 % Rotamer: Outliers : 3.83 % Allowed : 18.15 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 4728 helix: 1.17 (0.10), residues: 2679 sheet: -0.38 (0.30), residues: 304 loop : -0.67 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 30 TYR 0.022 0.002 TYR M 197 PHE 0.026 0.002 PHE L 341 TRP 0.021 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01193 (38762) covalent geometry : angle 2.17860 (52577) hydrogen bonds : bond 0.05360 ( 1700) hydrogen bonds : angle 4.25338 ( 5100) metal coordination : bond 0.04067 ( 36) metal coordination : angle 28.92974 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 471 time to evaluate : 1.253 Fit side-chains REVERT: F 30 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8240 (mtm180) REVERT: F 32 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8832 (ptmt) REVERT: F 48 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8397 (t0) REVERT: F 255 ARG cc_start: 0.8940 (mtt-85) cc_final: 0.8531 (mtt-85) REVERT: G 56 GLN cc_start: 0.7684 (pt0) cc_final: 0.7369 (mm-40) REVERT: G 332 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6726 (tm-30) REVERT: G 496 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8524 (mptp) REVERT: G 859 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.8050 (mtm110) REVERT: G 874 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: C 194 MET cc_start: 0.8869 (mmt) cc_final: 0.8529 (mmt) REVERT: C 238 ASP cc_start: 0.8090 (p0) cc_final: 0.7879 (p0) REVERT: C 482 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7735 (pt0) REVERT: C 597 ASP cc_start: 0.8716 (t0) cc_final: 0.8238 (t0) REVERT: B 13 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6949 (mm-30) REVERT: B 44 ASP cc_start: 0.8485 (m-30) cc_final: 0.8246 (m-30) REVERT: B 57 TYR cc_start: 0.8958 (t80) cc_final: 0.8738 (t80) REVERT: I 126 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8665 (mttm) REVERT: H 36 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: H 228 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: H 242 TYR cc_start: 0.8806 (m-80) cc_final: 0.8337 (m-80) REVERT: L 1 MET cc_start: 0.7801 (tpp) cc_final: 0.7053 (mmm) REVERT: L 127 MET cc_start: 0.8722 (tpt) cc_final: 0.8452 (tpt) REVERT: L 241 ASP cc_start: 0.7738 (m-30) cc_final: 0.7384 (m-30) REVERT: L 571 ILE cc_start: 0.7672 (mt) cc_final: 0.7336 (mp) REVERT: M 74 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7439 (tpt170) REVERT: M 122 TRP cc_start: 0.7201 (t-100) cc_final: 0.6201 (t60) REVERT: M 304 MET cc_start: 0.8805 (mmm) cc_final: 0.8563 (mmm) REVERT: K 87 ARG cc_start: 0.7922 (tmt90) cc_final: 0.7670 (tmt90) REVERT: J 55 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: J 91 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7915 (pp30) outliers start: 149 outliers final: 76 residues processed: 557 average time/residue: 0.6983 time to fit residues: 472.0453 Evaluate side-chains 540 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 450 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 156 TYR Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 153 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 346 optimal weight: 20.0000 chunk 327 optimal weight: 5.9990 chunk 101 optimal weight: 0.0870 chunk 71 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 260 optimal weight: 0.9990 chunk 380 optimal weight: 10.0000 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 159 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 745 GLN G 834 GLN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 403 ASN M 495 ASN M 502 ASN K 40 ASN K 88 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.068740 restraints weight = 54683.726| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.17 r_work: 0.2823 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.242 38798 Z= 0.396 Angle : 2.486 52.211 52670 Z= 1.428 Chirality : 0.441 6.458 5853 Planarity : 0.004 0.049 6572 Dihedral : 9.029 97.531 5755 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.42 % Allowed : 18.74 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 4728 helix: 1.33 (0.10), residues: 2670 sheet: -0.43 (0.30), residues: 311 loop : -0.62 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 30 TYR 0.025 0.002 TYR H 156 PHE 0.027 0.001 PHE L 341 TRP 0.020 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01143 (38762) covalent geometry : angle 2.16876 (52577) hydrogen bonds : bond 0.04909 ( 1700) hydrogen bonds : angle 4.15922 ( 5100) metal coordination : bond 0.03246 ( 36) metal coordination : angle 29.01744 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 471 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8197 (mtm180) REVERT: F 182 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8376 (tm-30) REVERT: F 255 ARG cc_start: 0.8925 (mtt-85) cc_final: 0.8537 (mtt-85) REVERT: F 321 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8637 (tp) REVERT: G 56 GLN cc_start: 0.7705 (pt0) cc_final: 0.7451 (mm-40) REVERT: G 332 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6655 (tm-30) REVERT: G 496 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8555 (mptp) REVERT: G 874 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: C 240 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7142 (tp30) REVERT: C 298 THR cc_start: 0.8951 (m) cc_final: 0.8643 (t) REVERT: C 482 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7756 (pt0) REVERT: C 597 ASP cc_start: 0.8703 (t0) cc_final: 0.8193 (t0) REVERT: B 13 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6999 (mm-30) REVERT: B 44 ASP cc_start: 0.8495 (m-30) cc_final: 0.8286 (m-30) REVERT: I 126 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8640 (mttm) REVERT: H 36 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: H 206 VAL cc_start: 0.7851 (t) cc_final: 0.7617 (t) REVERT: H 228 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: H 242 TYR cc_start: 0.8792 (m-80) cc_final: 0.8324 (m-80) REVERT: L 1 MET cc_start: 0.7949 (tpp) cc_final: 0.7178 (mmm) REVERT: L 127 MET cc_start: 0.8693 (tpt) cc_final: 0.8408 (tpt) REVERT: L 241 ASP cc_start: 0.7750 (m-30) cc_final: 0.7415 (m-30) REVERT: L 571 ILE cc_start: 0.7642 (mt) cc_final: 0.7306 (mp) REVERT: M 74 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7429 (tpt170) REVERT: M 122 TRP cc_start: 0.7188 (t-100) cc_final: 0.6163 (t60) REVERT: M 224 MET cc_start: 0.8473 (tmm) cc_final: 0.8010 (tmm) REVERT: N 118 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8151 (tp) REVERT: N 280 SER cc_start: 0.8691 (t) cc_final: 0.8088 (m) REVERT: J 91 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7908 (pp30) outliers start: 133 outliers final: 66 residues processed: 550 average time/residue: 0.7166 time to fit residues: 477.5713 Evaluate side-chains 537 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 456 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 388 optimal weight: 10.0000 chunk 275 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 142 optimal weight: 0.0770 chunk 132 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 442 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 overall best weight: 5.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 159 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 834 GLN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 348 HIS M 495 ASN M 502 ASN K 40 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.066867 restraints weight = 53835.594| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.18 r_work: 0.2782 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.240 38798 Z= 0.439 Angle : 2.500 50.625 52670 Z= 1.435 Chirality : 0.445 6.520 5853 Planarity : 0.005 0.066 6572 Dihedral : 9.240 95.430 5753 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.92 % Favored : 97.06 % Rotamer: Outliers : 3.65 % Allowed : 18.89 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.12), residues: 4728 helix: 1.14 (0.10), residues: 2687 sheet: -0.58 (0.30), residues: 304 loop : -0.66 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 30 TYR 0.022 0.002 TYR L 428 PHE 0.026 0.002 PHE L 341 TRP 0.023 0.002 TRP L 143 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01224 (38762) covalent geometry : angle 2.18732 (52577) hydrogen bonds : bond 0.05660 ( 1700) hydrogen bonds : angle 4.34068 ( 5100) metal coordination : bond 0.04131 ( 36) metal coordination : angle 28.90687 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 461 time to evaluate : 1.646 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8250 (mtm180) REVERT: F 48 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8456 (t0) REVERT: F 182 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: F 255 ARG cc_start: 0.8975 (mtt-85) cc_final: 0.8543 (mtt-85) REVERT: F 321 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8796 (tm) REVERT: G 56 GLN cc_start: 0.7896 (pt0) cc_final: 0.7579 (mm110) REVERT: G 496 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8468 (mptp) REVERT: G 874 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: C 105 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8873 (mm) REVERT: C 240 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7149 (tp30) REVERT: C 482 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7712 (pt0) REVERT: C 597 ASP cc_start: 0.8712 (t0) cc_final: 0.8331 (t0) REVERT: B 13 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: B 44 ASP cc_start: 0.8511 (m-30) cc_final: 0.8283 (m-30) REVERT: B 166 MET cc_start: 0.9193 (mtt) cc_final: 0.8937 (mtp) REVERT: I 126 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8702 (mttm) REVERT: H 36 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: H 228 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: H 242 TYR cc_start: 0.8850 (m-80) cc_final: 0.8425 (m-80) REVERT: A 134 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.6003 (ptt180) REVERT: L 1 MET cc_start: 0.8062 (tpp) cc_final: 0.7409 (mmm) REVERT: L 571 ILE cc_start: 0.7837 (mt) cc_final: 0.7553 (mt) REVERT: M 2 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8182 (mp) REVERT: M 38 LEU cc_start: 0.8180 (tp) cc_final: 0.7884 (tp) REVERT: M 74 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7475 (tpt170) REVERT: M 122 TRP cc_start: 0.7282 (t-100) cc_final: 0.6293 (t60) REVERT: M 168 ILE cc_start: 0.8549 (mt) cc_final: 0.8256 (mm) REVERT: M 185 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.9108 (ttm) REVERT: M 224 MET cc_start: 0.8514 (tmm) cc_final: 0.8079 (tmm) REVERT: M 235 MET cc_start: 0.9104 (tpp) cc_final: 0.8642 (ttm) REVERT: N 118 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8229 (tp) REVERT: N 219 SER cc_start: 0.8871 (m) cc_final: 0.8563 (p) REVERT: N 280 SER cc_start: 0.8761 (t) cc_final: 0.8176 (m) REVERT: N 450 TYR cc_start: 0.8775 (t80) cc_final: 0.8323 (t80) REVERT: N 463 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8563 (tt) REVERT: J 91 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7919 (pp30) outliers start: 142 outliers final: 75 residues processed: 548 average time/residue: 0.7321 time to fit residues: 487.0604 Evaluate side-chains 544 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 449 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 487 HIS Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 274 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 460 optimal weight: 3.9990 chunk 412 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 433 optimal weight: 10.0000 chunk 307 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 428 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 159 ASN G 103 HIS ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 495 ASN M 502 ASN K 40 ASN K 88 GLN J 75 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.069438 restraints weight = 53974.165| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.18 r_work: 0.2838 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 38798 Z= 0.387 Angle : 2.486 52.431 52670 Z= 1.427 Chirality : 0.441 6.429 5853 Planarity : 0.004 0.053 6572 Dihedral : 8.897 93.384 5753 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.83 % Allowed : 20.00 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.12), residues: 4728 helix: 1.43 (0.10), residues: 2680 sheet: -0.51 (0.30), residues: 311 loop : -0.59 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 804 TYR 0.024 0.001 TYR L 428 PHE 0.028 0.001 PHE L 341 TRP 0.023 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01127 (38762) covalent geometry : angle 2.16673 (52577) hydrogen bonds : bond 0.04708 ( 1700) hydrogen bonds : angle 4.14198 ( 5100) metal coordination : bond 0.02991 ( 36) metal coordination : angle 29.09001 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 466 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8204 (mtm180) REVERT: F 182 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: F 298 ASP cc_start: 0.8455 (m-30) cc_final: 0.8185 (m-30) REVERT: C 80 MET cc_start: 0.9072 (ttt) cc_final: 0.8795 (ttm) REVERT: C 240 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7119 (tp30) REVERT: C 298 THR cc_start: 0.8914 (m) cc_final: 0.8605 (t) REVERT: C 597 ASP cc_start: 0.8672 (t0) cc_final: 0.8326 (t0) REVERT: B 21 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8465 (tptt) REVERT: B 44 ASP cc_start: 0.8501 (m-30) cc_final: 0.8300 (m-30) REVERT: B 57 TYR cc_start: 0.8957 (t80) cc_final: 0.8678 (t80) REVERT: B 166 MET cc_start: 0.9146 (mtt) cc_final: 0.8859 (mtp) REVERT: I 126 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8683 (mttm) REVERT: H 36 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: H 228 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: H 242 TYR cc_start: 0.8841 (m-80) cc_final: 0.8411 (m-80) REVERT: A 134 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5902 (ptt180) REVERT: L 1 MET cc_start: 0.8089 (tpp) cc_final: 0.7360 (mmm) REVERT: L 127 MET cc_start: 0.8570 (tpt) cc_final: 0.8341 (tpt) REVERT: L 571 ILE cc_start: 0.7764 (mt) cc_final: 0.7440 (mp) REVERT: M 74 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7530 (tpt170) REVERT: M 122 TRP cc_start: 0.7276 (t-100) cc_final: 0.6323 (t60) REVERT: M 224 MET cc_start: 0.8484 (tmm) cc_final: 0.8033 (tmm) REVERT: M 382 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8019 (mmtt) REVERT: N 118 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8140 (tp) REVERT: N 219 SER cc_start: 0.8832 (m) cc_final: 0.8521 (p) REVERT: N 280 SER cc_start: 0.8718 (t) cc_final: 0.8151 (m) REVERT: K 31 MET cc_start: 0.8550 (mtp) cc_final: 0.8345 (mtp) REVERT: J 55 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: J 91 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7881 (pp30) outliers start: 110 outliers final: 63 residues processed: 535 average time/residue: 0.7514 time to fit residues: 487.4259 Evaluate side-chains 530 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 454 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 156 TYR Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 382 LYS Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 49 optimal weight: 9.9990 chunk 237 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 446 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 345 optimal weight: 20.0000 chunk 456 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 159 ASN G 56 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 495 ASN M 502 ASN K 40 ASN J 75 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.086703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.069842 restraints weight = 53851.945| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.18 r_work: 0.2846 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38798 Z= 0.386 Angle : 2.485 51.431 52670 Z= 1.427 Chirality : 0.440 6.426 5853 Planarity : 0.004 0.055 6572 Dihedral : 8.712 92.142 5750 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.67 % Allowed : 20.33 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.12), residues: 4728 helix: 1.52 (0.10), residues: 2677 sheet: -0.43 (0.30), residues: 320 loop : -0.53 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 804 TYR 0.023 0.001 TYR N 424 PHE 0.027 0.001 PHE L 341 TRP 0.018 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01126 (38762) covalent geometry : angle 2.16622 (52577) hydrogen bonds : bond 0.04583 ( 1700) hydrogen bonds : angle 4.08487 ( 5100) metal coordination : bond 0.02901 ( 36) metal coordination : angle 29.04643 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 460 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8193 (mtm180) REVERT: F 182 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8329 (tm-30) REVERT: F 298 ASP cc_start: 0.8478 (m-30) cc_final: 0.8209 (m-30) REVERT: F 321 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8590 (tp) REVERT: E 47 ARG cc_start: 0.8793 (mtt90) cc_final: 0.8427 (mtt90) REVERT: G 859 ARG cc_start: 0.8523 (mtp85) cc_final: 0.8209 (mtp-110) REVERT: C 53 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8359 (mmmt) REVERT: C 80 MET cc_start: 0.9077 (ttt) cc_final: 0.8834 (ttm) REVERT: C 105 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8852 (mm) REVERT: C 240 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7041 (tp30) REVERT: C 298 THR cc_start: 0.8923 (m) cc_final: 0.8615 (t) REVERT: C 597 ASP cc_start: 0.8663 (t0) cc_final: 0.8316 (t0) REVERT: B 13 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7032 (mm-30) REVERT: B 44 ASP cc_start: 0.8456 (m-30) cc_final: 0.8241 (m-30) REVERT: B 166 MET cc_start: 0.9101 (mtt) cc_final: 0.8651 (mtt) REVERT: B 194 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7541 (mtp85) REVERT: I 126 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8660 (mttm) REVERT: H 36 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: H 160 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8516 (tp) REVERT: H 165 MET cc_start: 0.8320 (mmp) cc_final: 0.7863 (mmp) REVERT: H 228 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: H 242 TYR cc_start: 0.8816 (m-80) cc_final: 0.8454 (m-80) REVERT: A 134 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.5847 (ptt180) REVERT: L 1 MET cc_start: 0.8119 (tpp) cc_final: 0.7430 (mmm) REVERT: L 127 MET cc_start: 0.8572 (tpt) cc_final: 0.8263 (tpt) REVERT: L 571 ILE cc_start: 0.7785 (mt) cc_final: 0.7452 (mp) REVERT: M 74 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7490 (tpt170) REVERT: M 122 TRP cc_start: 0.7228 (t-100) cc_final: 0.6231 (t60) REVERT: M 185 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.9028 (ttm) REVERT: M 224 MET cc_start: 0.8484 (tmm) cc_final: 0.8019 (tmm) REVERT: M 235 MET cc_start: 0.9024 (tpp) cc_final: 0.8546 (tpp) REVERT: N 118 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8096 (tp) REVERT: N 219 SER cc_start: 0.8818 (m) cc_final: 0.8489 (p) REVERT: N 280 SER cc_start: 0.8661 (t) cc_final: 0.8064 (m) REVERT: J 91 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7877 (pp30) outliers start: 104 outliers final: 58 residues processed: 527 average time/residue: 0.7180 time to fit residues: 457.8102 Evaluate side-chains 522 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 449 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 70 optimal weight: 8.9990 chunk 308 optimal weight: 9.9990 chunk 323 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 364 optimal weight: 5.9990 chunk 370 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 333 optimal weight: 5.9990 chunk 286 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN F 159 ASN E 56 HIS G 56 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 361 GLN M 495 ASN M 502 ASN K 88 GLN J 75 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.085803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.068826 restraints weight = 54538.291| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.19 r_work: 0.2825 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38798 Z= 0.398 Angle : 2.490 50.632 52670 Z= 1.430 Chirality : 0.442 6.473 5853 Planarity : 0.004 0.057 6572 Dihedral : 8.719 90.687 5747 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.72 % Allowed : 20.64 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.12), residues: 4728 helix: 1.46 (0.10), residues: 2673 sheet: -0.39 (0.30), residues: 309 loop : -0.53 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 804 TYR 0.020 0.002 TYR L 428 PHE 0.026 0.001 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01147 (38762) covalent geometry : angle 2.17434 (52577) hydrogen bonds : bond 0.04898 ( 1700) hydrogen bonds : angle 4.14135 ( 5100) metal coordination : bond 0.03450 ( 36) metal coordination : angle 28.96031 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 460 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8208 (mtm180) REVERT: F 182 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8370 (tm-30) REVERT: F 321 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8607 (tp) REVERT: G 192 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: G 332 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: G 496 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8515 (mmmt) REVERT: G 859 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8232 (mtp-110) REVERT: C 53 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8345 (mmmt) REVERT: C 80 MET cc_start: 0.9087 (ttt) cc_final: 0.8830 (ttm) REVERT: C 105 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8852 (mm) REVERT: C 240 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7122 (tp30) REVERT: C 597 ASP cc_start: 0.8684 (t0) cc_final: 0.8206 (t0) REVERT: B 13 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.6972 (mm-30) REVERT: B 44 ASP cc_start: 0.8442 (m-30) cc_final: 0.8221 (m-30) REVERT: B 57 TYR cc_start: 0.9024 (t80) cc_final: 0.8742 (t80) REVERT: B 166 MET cc_start: 0.9153 (mtt) cc_final: 0.8851 (mtp) REVERT: B 194 ARG cc_start: 0.7858 (mmm160) cc_final: 0.7540 (mtp85) REVERT: B 196 ASN cc_start: 0.8679 (m110) cc_final: 0.8375 (m-40) REVERT: I 126 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8672 (mttm) REVERT: H 36 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: H 160 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8517 (tp) REVERT: H 228 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: H 242 TYR cc_start: 0.8826 (m-80) cc_final: 0.8496 (m-80) REVERT: A 134 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5906 (ptt180) REVERT: L 1 MET cc_start: 0.8173 (tpp) cc_final: 0.7633 (mmm) REVERT: L 127 MET cc_start: 0.8612 (tpt) cc_final: 0.8242 (tpt) REVERT: L 571 ILE cc_start: 0.7774 (mt) cc_final: 0.7429 (mp) REVERT: M 74 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7503 (tpt170) REVERT: M 122 TRP cc_start: 0.7231 (t-100) cc_final: 0.6228 (t60) REVERT: M 185 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.9069 (ttm) REVERT: M 224 MET cc_start: 0.8464 (tmm) cc_final: 0.8004 (tmm) REVERT: M 235 MET cc_start: 0.9063 (tpp) cc_final: 0.8558 (tpp) REVERT: M 382 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8121 (mmtt) REVERT: M 409 MET cc_start: 0.8869 (mtp) cc_final: 0.8666 (mtp) REVERT: N 219 SER cc_start: 0.8835 (m) cc_final: 0.8507 (p) REVERT: N 280 SER cc_start: 0.8661 (t) cc_final: 0.8062 (m) REVERT: J 91 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7899 (pp30) outliers start: 106 outliers final: 64 residues processed: 528 average time/residue: 0.7471 time to fit residues: 477.2011 Evaluate side-chains 535 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 453 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU 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 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 332 GLU Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 382 LYS Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 320 optimal weight: 9.9990 chunk 368 optimal weight: 9.9990 chunk 389 optimal weight: 4.9990 chunk 365 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 314 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 433 optimal weight: 1.9990 chunk 414 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 56 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 834 GLN H 323 GLN M 335 GLN M 502 ASN J 75 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.068390 restraints weight = 53899.108| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.17 r_work: 0.2813 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 38798 Z= 0.407 Angle : 2.495 50.629 52670 Z= 1.432 Chirality : 0.443 6.513 5853 Planarity : 0.004 0.055 6572 Dihedral : 8.758 89.717 5747 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.34 % Allowed : 21.16 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.12), residues: 4728 helix: 1.40 (0.10), residues: 2682 sheet: -0.41 (0.30), residues: 312 loop : -0.54 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 804 TYR 0.020 0.002 TYR L 428 PHE 0.027 0.002 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01165 (38762) covalent geometry : angle 2.18096 (52577) hydrogen bonds : bond 0.05084 ( 1700) hydrogen bonds : angle 4.20347 ( 5100) metal coordination : bond 0.03789 ( 36) metal coordination : angle 28.94225 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9456 Ramachandran restraints generated. 4728 Oldfield, 0 Emsley, 4728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 455 time to evaluate : 1.466 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8220 (mtm180) REVERT: F 182 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: G 192 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8291 (mp0) REVERT: G 859 ARG cc_start: 0.8500 (mtp85) cc_final: 0.8204 (mtp-110) REVERT: C 53 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8446 (mmmt) REVERT: C 80 MET cc_start: 0.9094 (ttt) cc_final: 0.8828 (ttm) REVERT: C 105 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8875 (mm) REVERT: C 240 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: C 597 ASP cc_start: 0.8674 (t0) cc_final: 0.8175 (t0) REVERT: B 13 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6981 (mm-30) REVERT: B 44 ASP cc_start: 0.8445 (m-30) cc_final: 0.8232 (m-30) REVERT: B 57 TYR cc_start: 0.9051 (t80) cc_final: 0.8851 (t80) REVERT: B 166 MET cc_start: 0.9193 (mtt) cc_final: 0.8945 (mtp) REVERT: B 194 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7586 (mtp85) REVERT: I 126 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8682 (mttm) REVERT: H 36 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: H 160 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8537 (tp) REVERT: H 228 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8328 (mp0) REVERT: H 242 TYR cc_start: 0.8857 (m-80) cc_final: 0.8463 (m-80) REVERT: A 134 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5978 (ptt180) REVERT: L 1 MET cc_start: 0.8182 (tpp) cc_final: 0.7683 (mmm) REVERT: L 127 MET cc_start: 0.8681 (tpt) cc_final: 0.8299 (tpt) REVERT: L 571 ILE cc_start: 0.7855 (mt) cc_final: 0.7553 (mt) REVERT: M 74 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7513 (tpt170) REVERT: M 122 TRP cc_start: 0.7275 (t-100) cc_final: 0.6322 (t60) REVERT: M 185 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.9067 (ttm) REVERT: M 381 MET cc_start: 0.8263 (ptt) cc_final: 0.8045 (ptt) REVERT: M 382 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8143 (mmtt) REVERT: N 219 SER cc_start: 0.8852 (m) cc_final: 0.8543 (p) REVERT: N 280 SER cc_start: 0.8717 (t) cc_final: 0.8132 (m) REVERT: N 480 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8106 (mm) REVERT: J 91 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7908 (pp30) outliers start: 91 outliers final: 62 residues processed: 515 average time/residue: 0.7629 time to fit residues: 472.6904 Evaluate side-chains 527 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 449 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 425 GLN Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 223 MET Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 566 VAL Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 734 THR Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 582 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 156 TYR Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 478 VAL Chi-restraints excluded: chain L residue 511 LEU Chi-restraints excluded: chain L residue 598 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 185 MET Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 382 LYS Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 263 VAL Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 388 MET Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain N residue 480 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 75 ASN Chi-restraints excluded: chain J residue 91 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 289 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 352 optimal weight: 8.9990 chunk 456 optimal weight: 1.9990 chunk 309 optimal weight: 0.7980 chunk 332 optimal weight: 7.9990 chunk 421 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 329 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 834 GLN H 323 GLN M 335 GLN M 502 ASN K 88 GLN J 75 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.068215 restraints weight = 54057.225| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.19 r_work: 0.2812 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 38798 Z= 0.407 Angle : 2.496 50.631 52670 Z= 1.432 Chirality : 0.443 6.513 5853 Planarity : 0.004 0.056 6572 Dihedral : 8.752 89.217 5745 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.34 % Allowed : 21.26 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.12), residues: 4728 helix: 1.39 (0.10), residues: 2682 sheet: -0.46 (0.30), residues: 315 loop : -0.53 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 804 TYR 0.020 0.002 TYR L 428 PHE 0.027 0.002 PHE L 341 TRP 0.020 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01164 (38762) covalent geometry : angle 2.18201 (52577) hydrogen bonds : bond 0.05106 ( 1700) hydrogen bonds : angle 4.21256 ( 5100) metal coordination : bond 0.03746 ( 36) metal coordination : angle 28.94744 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15360.35 seconds wall clock time: 262 minutes 16.17 seconds (15736.17 seconds total)