Starting phenix.real_space_refine on Mon Jul 6 17:32:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z80_14540/07_2026/7z80_14540.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z80_14540/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7z80_14540/07_2026/7z80_14540.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z80_14540/07_2026/7z80_14540.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z80_14540/07_2026/7z80_14540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z80_14540/07_2026/7z80_14540.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z80_14540/07_2026/7z80_14540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z80_14540/07_2026/7z80_14540.map" } 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-dev-6108/lib/python3.11/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: 6.66, per 1000 atoms: 0.18 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: 3.12 Conformation dependent library (CDL) restraints added in 1.3 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: 0.88 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: 5.98 Time building geometry restraints manager: 4.21 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=" 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 bond pdb=" O13 3PE M1001 " pdb=" P 3PE M1001 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.67e+00 bond pdb=" O13 3PE L 803 " pdb=" P 3PE L 803 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.65e+00 bond pdb=" O13 3PE L 805 " pdb=" P 3PE L 805 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.58e+00 bond pdb=" O13 3PE C 701 " pdb=" P 3PE C 701 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.53e+00 ... (remaining 38757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 52040 3.11 - 6.22: 429 6.22 - 9.33: 86 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 - 34.01: 21900 34.01 - 68.02: 752 68.02 - 102.03: 50 102.03 - 136.04: 0 136.04 - 170.05: 1 Dihedral angle restraints: 22703 sinusoidal: 9093 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=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 87.54 170.05 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 22700 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: 6571 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 6568 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 34.320 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 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= 0.214 Angle : 0.803 15.544 52670 Z= 0.397 Chirality : 1.462 21.171 5853 Planarity : 0.006 0.119 6571 Dihedral : 16.185 170.055 13999 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/Z covalent geometry : bond 0.00452 / 0.21 (38762) covalent geometry : angle 0.78952 / 0.40 (52577) hydrogen bonds : bond 0.05019 / 3.33 ( 1700) hydrogen bonds : angle 4.61783 / 3.31 ( 5100) metal coordination : bond 0.05852 / 3.80 ( 36) metal coordination : angle 3.56626 / 2.56 ( 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 : 1.167 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: 0.6254 time to fit residues: 419.2507 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 : 1.448 ------------------------------------------------------------------------------- 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... 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 = 0.3306 r_free = 0.3306 target = 0.087947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.071116 restraints weight = 55425.278| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.19 r_work: 0.2874 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.262 38798 Z= 0.395 Angle : 2.483 54.324 52670 Z= 1.426 Chirality : 0.444 6.490 5853 Planarity : 0.004 0.052 6571 Dihedral : 7.801 174.073 5644 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.21 % Allowed : 17.48 % Favored : 79.31 % 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: 0.31 (0.12), residues: 4728 helix: 1.00 (0.10), residues: 2669 sheet: -0.44 (0.28), residues: 325 loop : -0.85 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 64 TYR 0.022 0.002 TYR L 428 PHE 0.027 0.001 PHE L 341 TRP 0.017 0.001 TRP L 143 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01139 / 0.39 (38762) covalent geometry : angle 2.16498 / 1.42 (52577) hydrogen bonds : bond 0.04662 / 3.10 ( 1700) hydrogen bonds : angle 4.14838 / 2.98 ( 5100) metal coordination : bond 0.04194 / 2.52 ( 36) metal coordination : angle 29.02084 / 20.14 ( 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 600 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 475 time to evaluate : 1.088 Fit side-chains REVERT: F 48 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8352 (t0) REVERT: G 332 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: G 496 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8558 (mptp) REVERT: C 482 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7765 (pt0) REVERT: B 57 TYR cc_start: 0.8774 (t80) cc_final: 0.8547 (t80) REVERT: I 126 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8647 (mttm) REVERT: H 36 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: H 122 MET cc_start: 0.8698 (mmp) cc_final: 0.8320 (mmp) REVERT: H 228 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: H 242 TYR cc_start: 0.8719 (m-80) cc_final: 0.8263 (m-80) REVERT: L 127 MET cc_start: 0.8508 (tpt) cc_final: 0.8291 (tpt) REVERT: M 185 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.9078 (ttm) REVERT: M 304 MET cc_start: 0.8642 (mmm) cc_final: 0.8189 (mmp) REVERT: M 372 ARG cc_start: 0.7996 (mtm180) cc_final: 0.7509 (mtm180) REVERT: N 255 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7768 (mtm) REVERT: K 1 MET cc_start: 0.7550 (tmm) cc_final: 0.6764 (tmm) REVERT: J 1 MET cc_start: 0.7969 (ttm) cc_final: 0.7642 (ttm) outliers start: 125 outliers final: 54 residues processed: 547 average time/residue: 0.6674 time to fit residues: 444.9232 Evaluate side-chains 514 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 451 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 855 ASN 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 B residue 197 MET Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 159 ASP 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 83 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: 10.0000 chunk 91 optimal weight: 7.9990 chunk 439 optimal weight: 6.9990 chunk 398 optimal weight: 50.0000 chunk 58 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 338 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 670 GLN ** G 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 834 GLN C 31 ASN C 359 HIS B 111 GLN H 312 ASN A 47 ASN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 301 GLN ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 502 ASN N 291 GLN K 40 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.083619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.066181 restraints weight = 55014.396| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.23 r_work: 0.2765 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.245 38798 Z= 0.458 Angle : 2.509 51.413 52670 Z= 1.439 Chirality : 0.446 6.573 5853 Planarity : 0.006 0.086 6571 Dihedral : 8.305 177.074 5587 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Rotamer: Outliers : 4.14 % Allowed : 17.17 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.12), residues: 4728 helix: 0.88 (0.10), residues: 2692 sheet: -0.53 (0.29), residues: 313 loop : -0.76 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG K 87 TYR 0.024 0.003 TYR L 106 PHE 0.026 0.002 PHE L 341 TRP 0.021 0.002 TRP L 143 HIS 0.009 0.002 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01261 / 0.46 (38762) covalent geometry : angle 2.19743 / 1.44 (52577) hydrogen bonds : bond 0.06040 / 3.98 ( 1700) hydrogen bonds : angle 4.42864 / 3.20 ( 5100) metal coordination : bond 0.05093 / 3.15 ( 36) metal coordination : angle 28.89810 / 20.15 ( 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 635 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 474 time to evaluate : 0.962 Fit side-chains REVERT: F 32 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8852 (ptmt) REVERT: F 48 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8389 (t0) REVERT: G 56 GLN cc_start: 0.7710 (pt0) cc_final: 0.7387 (mm-40) REVERT: G 496 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8596 (mptp) REVERT: G 874 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: C 482 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7745 (pt0) REVERT: C 545 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8535 (t) REVERT: C 597 ASP cc_start: 0.8741 (t0) cc_final: 0.8261 (t0) REVERT: B 13 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6929 (mm-30) REVERT: B 57 TYR cc_start: 0.8978 (t80) cc_final: 0.8747 (t80) REVERT: I 126 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8736 (mttm) REVERT: H 36 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: H 122 MET cc_start: 0.8869 (mmp) cc_final: 0.8483 (mmp) REVERT: H 228 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: H 242 TYR cc_start: 0.8858 (m-80) cc_final: 0.8498 (m-80) REVERT: A 134 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.6190 (ptt180) REVERT: L 571 ILE cc_start: 0.7786 (mt) cc_final: 0.7468 (mp) REVERT: M 74 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7483 (tpt170) REVERT: M 136 MET cc_start: 0.8880 (mmm) cc_final: 0.8470 (mmm) REVERT: M 235 MET cc_start: 0.9157 (tpp) cc_final: 0.8814 (ttm) REVERT: M 398 MET cc_start: 0.8846 (tpt) cc_final: 0.8567 (tpt) REVERT: K 1 MET cc_start: 0.7291 (tmm) cc_final: 0.7055 (ppp) REVERT: J 91 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7916 (pp30) REVERT: J 109 TYR cc_start: 0.8508 (t80) cc_final: 0.8297 (t80) outliers start: 161 outliers final: 71 residues processed: 572 average time/residue: 0.6589 time to fit residues: 459.4147 Evaluate side-chains 536 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 452 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 385 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 496 LYS 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 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 122 MET 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 206 VAL 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 7 THR 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 249 VAL Chi-restraints excluded: chain L residue 336 MET 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 518 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 393 VAL 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 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 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 K residue 77 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 117 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 441 optimal weight: 4.9990 chunk 435 optimal weight: 0.7980 chunk 363 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 423 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 745 GLN G 834 GLN H 312 ASN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN 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 = 0.3258 r_free = 0.3258 target = 0.085412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.068376 restraints weight = 54798.133| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.19 r_work: 0.2814 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38798 Z= 0.392 Angle : 2.486 53.236 52670 Z= 1.428 Chirality : 0.442 6.497 5853 Planarity : 0.004 0.049 6571 Dihedral : 8.004 176.704 5584 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.26 % Allowed : 18.82 % Favored : 77.92 % 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: 0.60 (0.12), residues: 4728 helix: 1.23 (0.10), residues: 2674 sheet: -0.44 (0.30), residues: 311 loop : -0.68 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 30 TYR 0.049 0.002 TYR H 156 PHE 0.028 0.001 PHE L 341 TRP 0.021 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01135 / 0.39 (38762) covalent geometry : angle 2.16757 / 1.43 (52577) hydrogen bonds : bond 0.05005 / 3.33 ( 1700) hydrogen bonds : angle 4.22253 / 3.04 ( 5100) metal coordination : bond 0.03188 / 1.91 ( 36) metal coordination : angle 29.06462 / 20.32 ( 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 595 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 468 time to evaluate : 1.360 Fit side-chains REVERT: F 48 ASP cc_start: 0.8644 (t70) cc_final: 0.8390 (t0) REVERT: F 255 ARG cc_start: 0.8927 (mtt-85) cc_final: 0.8538 (mtt-85) REVERT: G 56 GLN cc_start: 0.7694 (pt0) cc_final: 0.7380 (mm-40) REVERT: G 332 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: G 496 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8564 (mptp) REVERT: G 859 ARG cc_start: 0.8414 (mtp85) cc_final: 0.8210 (mtm110) REVERT: C 80 MET cc_start: 0.9071 (ttt) cc_final: 0.8811 (ttm) REVERT: C 194 MET cc_start: 0.8836 (mmt) cc_final: 0.8589 (mmt) REVERT: C 240 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7202 (tp30) REVERT: C 482 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7777 (pt0) REVERT: C 597 ASP cc_start: 0.8720 (t0) cc_final: 0.8315 (t0) REVERT: B 13 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6939 (mm-30) REVERT: B 44 ASP cc_start: 0.8497 (m-30) cc_final: 0.8269 (m-30) REVERT: I 126 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8635 (mttm) REVERT: H 36 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: H 122 MET cc_start: 0.8781 (mmp) cc_final: 0.8442 (mmp) REVERT: H 228 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: H 242 TYR cc_start: 0.8806 (m-80) cc_final: 0.8402 (m-80) REVERT: L 1 MET cc_start: 0.7792 (tpp) cc_final: 0.7081 (mmm) REVERT: L 127 MET cc_start: 0.8663 (tpt) cc_final: 0.8295 (tpt) REVERT: L 571 ILE cc_start: 0.7674 (mt) cc_final: 0.7353 (mp) REVERT: M 74 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7429 (tpt170) REVERT: M 122 TRP cc_start: 0.7198 (t-100) cc_final: 0.6195 (t60) REVERT: M 136 MET cc_start: 0.8816 (mmm) cc_final: 0.8452 (mmm) REVERT: M 185 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9093 (ttm) REVERT: M 224 MET cc_start: 0.8483 (tmm) cc_final: 0.8028 (tmm) REVERT: M 235 MET cc_start: 0.9108 (tpp) cc_final: 0.8831 (tpp) REVERT: M 304 MET cc_start: 0.8821 (mmm) cc_final: 0.8506 (mmm) REVERT: M 398 MET cc_start: 0.8782 (tpt) cc_final: 0.8566 (tpt) REVERT: N 280 SER cc_start: 0.8716 (t) cc_final: 0.8133 (m) REVERT: J 1 MET cc_start: 0.8105 (ttm) cc_final: 0.7571 (ttp) REVERT: J 91 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7884 (pp30) outliers start: 127 outliers final: 63 residues processed: 543 average time/residue: 0.6482 time to fit residues: 426.9375 Evaluate side-chains 526 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 452 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 229 LEU 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 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 405 GLU Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 496 LYS 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 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 325 THR 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 20 GLN Chi-restraints excluded: chain B residue 21 LYS 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 27 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 71 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 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 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 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 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 135 ILE Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 263 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 153 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 346 optimal weight: 20.0000 chunk 327 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 260 optimal weight: 5.9990 chunk 380 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 159 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN ** 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 502 ASN K 40 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.084837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.067911 restraints weight = 54680.143| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.20 r_work: 0.2797 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1645 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= 0.407 Angle : 2.490 51.542 52670 Z= 1.430 Chirality : 0.442 6.473 5853 Planarity : 0.005 0.052 6571 Dihedral : 7.979 176.373 5578 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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 : 0.02 % 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: 0.64 (0.12), residues: 4728 helix: 1.27 (0.10), residues: 2681 sheet: -0.53 (0.29), residues: 313 loop : -0.65 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 87 TYR 0.023 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/Z covalent geometry : bond 0.01164 / 0.41 (38762) covalent geometry : angle 2.17317 / 1.43 (52577) hydrogen bonds : bond 0.05133 / 3.41 ( 1700) hydrogen bonds : angle 4.22918 / 3.05 ( 5100) metal coordination : bond 0.03479 / 2.12 ( 36) metal coordination : angle 28.99120 / 20.34 ( 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 609 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 467 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8252 (mtm180) REVERT: F 48 ASP cc_start: 0.8660 (t70) cc_final: 0.8396 (t0) REVERT: F 182 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8343 (tm-30) REVERT: F 255 ARG cc_start: 0.8941 (mtt-85) cc_final: 0.8516 (mtt-85) REVERT: G 56 GLN cc_start: 0.7781 (pt0) cc_final: 0.7513 (mm-40) REVERT: G 332 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6726 (tm-30) REVERT: G 496 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8568 (mptp) REVERT: G 859 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8268 (mtm110) REVERT: G 874 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: C 80 MET cc_start: 0.9082 (ttt) cc_final: 0.8811 (ttm) REVERT: C 194 MET cc_start: 0.8884 (mmt) cc_final: 0.8574 (mmt) REVERT: C 240 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7165 (tp30) REVERT: C 482 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: C 597 ASP cc_start: 0.8721 (t0) cc_final: 0.8329 (t0) REVERT: B 13 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6961 (mm-30) REVERT: B 44 ASP cc_start: 0.8510 (m-30) cc_final: 0.8285 (m-30) REVERT: I 126 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8660 (mttm) REVERT: H 23 LEU cc_start: 0.8920 (mm) cc_final: 0.8720 (mt) REVERT: H 36 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: H 122 MET cc_start: 0.8833 (mmp) cc_final: 0.8477 (mmp) REVERT: H 228 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8435 (mp0) REVERT: H 242 TYR cc_start: 0.8826 (m-80) cc_final: 0.8357 (m-80) REVERT: L 1 MET cc_start: 0.7982 (tpp) cc_final: 0.7225 (mmm) REVERT: L 571 ILE cc_start: 0.7666 (mt) cc_final: 0.7341 (mp) REVERT: M 2 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8054 (mp) REVERT: M 38 LEU cc_start: 0.8122 (tp) cc_final: 0.7812 (tp) REVERT: M 74 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7408 (tpt170) REVERT: M 122 TRP cc_start: 0.7215 (t-100) cc_final: 0.6207 (t60) REVERT: M 136 MET cc_start: 0.8824 (mmm) cc_final: 0.8571 (mmp) REVERT: M 224 MET cc_start: 0.8495 (tmm) cc_final: 0.8040 (tmm) REVERT: M 235 MET cc_start: 0.9130 (tpp) cc_final: 0.8741 (ttm) REVERT: M 382 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7956 (mmtt) REVERT: M 398 MET cc_start: 0.8801 (tpt) cc_final: 0.8565 (tpt) REVERT: N 280 SER cc_start: 0.8713 (t) cc_final: 0.8130 (m) REVERT: K 26 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.7423 (ttm110) REVERT: J 91 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7906 (pp30) outliers start: 142 outliers final: 73 residues processed: 547 average time/residue: 0.6822 time to fit residues: 454.7870 Evaluate side-chains 538 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 450 time to evaluate : 1.436 ------------------------------------------------------------------------------- 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 94 MET 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 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 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 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 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 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 20 GLN 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 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 80 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 487 HIS Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain L residue 499 VAL 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 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 264 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 388 optimal weight: 8.9990 chunk 275 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 442 optimal weight: 8.9990 chunk 285 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 197 optimal weight: 0.9980 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 159 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.068278 restraints weight = 54944.216| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.22 r_work: 0.2810 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1668 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= 0.395 Angle : 2.487 52.487 52670 Z= 1.428 Chirality : 0.441 6.448 5853 Planarity : 0.004 0.052 6571 Dihedral : 7.839 176.213 5578 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.19 % Allowed : 19.51 % Favored : 77.30 % 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: 0.75 (0.12), residues: 4728 helix: 1.36 (0.10), residues: 2683 sheet: -0.50 (0.30), residues: 311 loop : -0.61 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 804 TYR 0.022 0.002 TYR L 428 PHE 0.027 0.001 PHE L 341 TRP 0.021 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01142 / 0.39 (38762) covalent geometry : angle 2.16750 / 1.42 (52577) hydrogen bonds : bond 0.04885 / 3.25 ( 1700) hydrogen bonds : angle 4.16873 / 3.01 ( 5100) metal coordination : bond 0.03229 / 1.98 ( 36) metal coordination : angle 29.08235 / 20.29 ( 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 586 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 462 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8227 (mtm180) REVERT: F 152 GLU cc_start: 0.8249 (pp20) cc_final: 0.8024 (pp20) REVERT: F 182 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8312 (tm-30) REVERT: F 255 ARG cc_start: 0.8936 (mtt-85) cc_final: 0.8543 (mtt-85) REVERT: G 56 GLN cc_start: 0.7811 (pt0) cc_final: 0.7584 (mm-40) REVERT: G 332 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: G 496 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8557 (mptp) REVERT: C 80 MET cc_start: 0.9072 (ttt) cc_final: 0.8814 (ttm) REVERT: C 105 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8836 (mm) REVERT: C 194 MET cc_start: 0.8864 (mmt) cc_final: 0.8572 (mmt) REVERT: C 240 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7119 (tp30) REVERT: C 482 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7766 (pt0) REVERT: C 597 ASP cc_start: 0.8700 (t0) cc_final: 0.8310 (t0) REVERT: B 44 ASP cc_start: 0.8496 (m-30) cc_final: 0.8260 (m-30) REVERT: I 126 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8674 (mttm) REVERT: H 23 LEU cc_start: 0.8930 (mm) cc_final: 0.8719 (mt) REVERT: H 36 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: H 122 MET cc_start: 0.8813 (mmp) cc_final: 0.8436 (mmp) REVERT: H 228 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: H 242 TYR cc_start: 0.8811 (m-80) cc_final: 0.8379 (m-80) REVERT: L 1 MET cc_start: 0.8006 (tpp) cc_final: 0.7367 (mmm) REVERT: L 127 MET cc_start: 0.8563 (tpt) cc_final: 0.8255 (tpt) REVERT: L 571 ILE cc_start: 0.7657 (mt) cc_final: 0.7333 (mp) REVERT: M 2 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8072 (mp) REVERT: M 74 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7440 (tpt170) REVERT: M 122 TRP cc_start: 0.7209 (t-100) cc_final: 0.6177 (t60) REVERT: M 136 MET cc_start: 0.8859 (mmm) cc_final: 0.8564 (mmp) REVERT: M 185 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9079 (ttm) REVERT: M 224 MET cc_start: 0.8487 (tmm) cc_final: 0.8020 (tmm) REVERT: M 235 MET cc_start: 0.9122 (tpp) cc_final: 0.8675 (ttm) REVERT: M 398 MET cc_start: 0.8785 (tpt) cc_final: 0.8534 (tpt) REVERT: N 219 SER cc_start: 0.8828 (m) cc_final: 0.8500 (p) REVERT: N 280 SER cc_start: 0.8709 (t) cc_final: 0.8135 (m) REVERT: K 26 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7429 (ttm110) REVERT: J 91 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7907 (pp30) outliers start: 124 outliers final: 68 residues processed: 537 average time/residue: 0.6497 time to fit residues: 426.4806 Evaluate side-chains 536 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 454 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 94 MET 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 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 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 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 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 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 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 L residue 3 MET Chi-restraints excluded: chain L residue 80 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 L residue 598 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 2 LEU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 274 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 460 optimal weight: 9.9990 chunk 412 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 433 optimal weight: 9.9990 chunk 307 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 428 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 159 ASN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** 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 J 75 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.068787 restraints weight = 54037.512| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.18 r_work: 0.2823 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1708 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= 0.395 Angle : 2.487 51.564 52670 Z= 1.428 Chirality : 0.441 6.445 5853 Planarity : 0.004 0.054 6571 Dihedral : 7.717 175.962 5576 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.24 % Allowed : 19.79 % Favored : 76.97 % 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: 0.81 (0.12), residues: 4728 helix: 1.42 (0.10), residues: 2676 sheet: -0.49 (0.29), residues: 314 loop : -0.58 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 804 TYR 0.021 0.002 TYR L 428 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/Z covalent geometry : bond 0.01142 / 0.39 (38762) covalent geometry : angle 2.16914 / 1.43 (52577) hydrogen bonds : bond 0.04879 / 3.25 ( 1700) hydrogen bonds : angle 4.15152 / 2.99 ( 5100) metal coordination : bond 0.03221 / 1.95 ( 36) metal coordination : angle 29.01658 / 20.29 ( 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 592 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 466 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8232 (mtm180) REVERT: F 182 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: F 255 ARG cc_start: 0.8933 (mtt-85) cc_final: 0.8566 (mtt-85) REVERT: F 321 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8629 (tp) REVERT: G 332 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: G 496 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8567 (mptp) REVERT: G 859 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8216 (mtp-110) REVERT: G 874 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: C 53 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8413 (mmmt) REVERT: C 80 MET cc_start: 0.9084 (ttt) cc_final: 0.8838 (ttm) REVERT: C 105 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8853 (mm) REVERT: C 240 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7069 (tp30) REVERT: C 482 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: C 597 ASP cc_start: 0.8680 (t0) cc_final: 0.8312 (t0) REVERT: B 13 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7024 (mm-30) REVERT: B 44 ASP cc_start: 0.8452 (m-30) cc_final: 0.8213 (m-30) REVERT: B 57 TYR cc_start: 0.9009 (t80) cc_final: 0.8701 (t80) REVERT: I 126 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8678 (mttm) REVERT: H 23 LEU cc_start: 0.8963 (mm) cc_final: 0.8743 (mt) REVERT: H 36 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: H 122 MET cc_start: 0.8834 (mmp) cc_final: 0.8460 (mmp) REVERT: H 160 LEU cc_start: 0.8942 (tp) cc_final: 0.8741 (tt) REVERT: H 228 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8319 (mp0) REVERT: H 242 TYR cc_start: 0.8829 (m-80) cc_final: 0.8426 (m-80) REVERT: L 1 MET cc_start: 0.8091 (tpp) cc_final: 0.7475 (mmm) REVERT: L 127 MET cc_start: 0.8656 (tpt) cc_final: 0.8246 (tpt) REVERT: L 571 ILE cc_start: 0.7783 (mt) cc_final: 0.7483 (mt) REVERT: M 74 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7501 (tpt170) REVERT: M 122 TRP cc_start: 0.7237 (t-100) cc_final: 0.6239 (t60) REVERT: M 136 MET cc_start: 0.8835 (mmm) cc_final: 0.8529 (mmp) REVERT: M 185 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.9083 (ttm) REVERT: M 224 MET cc_start: 0.8475 (tmm) cc_final: 0.8014 (tmm) REVERT: M 235 MET cc_start: 0.9115 (tpp) cc_final: 0.8720 (ttm) REVERT: M 304 MET cc_start: 0.8845 (mmm) cc_final: 0.8591 (mmm) REVERT: M 398 MET cc_start: 0.8769 (tpt) cc_final: 0.8517 (tpt) REVERT: N 219 SER cc_start: 0.8831 (m) cc_final: 0.8508 (p) REVERT: N 280 SER cc_start: 0.8701 (t) cc_final: 0.8103 (m) REVERT: K 26 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7476 (ttm110) REVERT: J 91 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7902 (pp30) outliers start: 126 outliers final: 73 residues processed: 542 average time/residue: 0.6778 time to fit residues: 447.3955 Evaluate side-chains 543 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 454 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 94 MET 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 181 VAL 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 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 566 VAL Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 735 MET Chi-restraints excluded: chain G residue 855 ASN 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 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 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 20 GLN Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 45 MET 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 L residue 29 VAL 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 336 MET 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 500 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 49 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 446 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 345 optimal weight: 20.0000 chunk 456 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 159 ASN G 56 GLN G 103 HIS ** 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 ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 361 GLN M 495 ASN M 502 ASN K 40 ASN K 88 GLN J 75 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.068705 restraints weight = 53710.683| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.17 r_work: 0.2821 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1767 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 : 2.487 50.675 52670 Z= 1.429 Chirality : 0.442 6.462 5853 Planarity : 0.004 0.054 6571 Dihedral : 7.661 175.911 5576 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.24 % Allowed : 19.92 % Favored : 76.84 % 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: 0.80 (0.12), residues: 4728 helix: 1.41 (0.10), residues: 2677 sheet: -0.55 (0.29), residues: 313 loop : -0.58 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 804 TYR 0.021 0.002 TYR L 428 PHE 0.027 0.001 PHE L 341 TRP 0.021 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01148 / 0.40 (38762) covalent geometry : angle 2.16992 / 1.43 (52577) hydrogen bonds : bond 0.04929 / 3.28 ( 1700) hydrogen bonds : angle 4.15962 / 3.00 ( 5100) metal coordination : bond 0.03458 / 2.18 ( 36) metal coordination : angle 28.98256 / 20.30 ( 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 591 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 465 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8225 (mtm180) REVERT: F 182 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: F 255 ARG cc_start: 0.8933 (mtt-85) cc_final: 0.8547 (mtt-85) REVERT: G 332 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: G 496 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8566 (mptp) REVERT: G 874 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: C 53 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8411 (mmmt) REVERT: C 80 MET cc_start: 0.9090 (ttt) cc_final: 0.8816 (ttm) REVERT: C 105 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8832 (mm) REVERT: C 238 ASP cc_start: 0.8055 (p0) cc_final: 0.7819 (p0) REVERT: C 240 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7071 (tp30) REVERT: C 482 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7749 (pt0) REVERT: C 597 ASP cc_start: 0.8679 (t0) cc_final: 0.8300 (t0) REVERT: B 13 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6969 (mm-30) REVERT: B 44 ASP cc_start: 0.8430 (m-30) cc_final: 0.8187 (m-30) REVERT: I 126 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8693 (mttm) REVERT: H 23 LEU cc_start: 0.8968 (mm) cc_final: 0.8742 (mt) REVERT: H 36 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: H 122 MET cc_start: 0.8830 (mmp) cc_final: 0.8462 (mmp) REVERT: H 156 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.8302 (p90) REVERT: H 160 LEU cc_start: 0.8910 (tp) cc_final: 0.8709 (tt) REVERT: H 228 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: H 242 TYR cc_start: 0.8829 (m-80) cc_final: 0.8425 (m-80) REVERT: L 1 MET cc_start: 0.8121 (tpp) cc_final: 0.7565 (mmm) REVERT: L 127 MET cc_start: 0.8669 (tpt) cc_final: 0.8247 (tpt) REVERT: L 571 ILE cc_start: 0.7779 (mt) cc_final: 0.7479 (mt) REVERT: M 2 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8131 (mp) REVERT: M 74 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7502 (tpt170) REVERT: M 122 TRP cc_start: 0.7236 (t-100) cc_final: 0.6250 (t60) REVERT: M 136 MET cc_start: 0.8842 (mmm) cc_final: 0.8535 (mmp) REVERT: M 185 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.9085 (ttm) REVERT: M 224 MET cc_start: 0.8472 (tmm) cc_final: 0.8010 (tmm) REVERT: M 235 MET cc_start: 0.9112 (tpp) cc_final: 0.8728 (ttm) REVERT: M 398 MET cc_start: 0.8772 (tpt) cc_final: 0.8523 (tpt) REVERT: N 219 SER cc_start: 0.8833 (m) cc_final: 0.8514 (p) REVERT: N 280 SER cc_start: 0.8701 (t) cc_final: 0.8106 (m) REVERT: K 26 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7491 (ttm110) REVERT: K 87 ARG cc_start: 0.7884 (tmt90) cc_final: 0.7643 (tmt90) REVERT: J 91 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7902 (pp30) outliers start: 126 outliers final: 71 residues processed: 541 average time/residue: 0.6422 time to fit residues: 423.5872 Evaluate side-chains 548 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 460 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 94 MET 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 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 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 566 VAL Chi-restraints excluded: chain G residue 670 GLN 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 272 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 325 THR 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 20 GLN 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 A residue 83 LEU Chi-restraints excluded: chain L residue 29 VAL 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 336 MET 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 500 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 2 LEU 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 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 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 65 VAL Chi-restraints excluded: chain J residue 70 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: 2.9990 chunk 308 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 364 optimal weight: 3.9990 chunk 370 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 333 optimal weight: 0.0050 chunk 286 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** G 834 GLN H 323 GLN ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 495 ASN M 502 ASN J 75 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.070348 restraints weight = 54462.668| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.17 r_work: 0.2857 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38798 Z= 0.384 Angle : 2.483 52.629 52670 Z= 1.426 Chirality : 0.440 6.435 5853 Planarity : 0.004 0.058 6571 Dihedral : 7.362 175.548 5571 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.16 % Allowed : 21.00 % Favored : 76.84 % 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: 0.98 (0.12), residues: 4728 helix: 1.57 (0.10), residues: 2671 sheet: -0.47 (0.29), residues: 322 loop : -0.53 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 804 TYR 0.023 0.001 TYR N 424 PHE 0.028 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/Z covalent geometry : bond 0.01123 / 0.38 (38762) covalent geometry : angle 2.16368 / 1.42 (52577) hydrogen bonds : bond 0.04461 / 2.98 ( 1700) hydrogen bonds : angle 4.05276 / 2.92 ( 5100) metal coordination : bond 0.02697 / 1.69 ( 36) metal coordination : angle 29.07436 / 20.38 ( 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 559 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 475 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8224 (mtm180) REVERT: F 182 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: F 298 ASP cc_start: 0.8428 (m-30) cc_final: 0.8128 (m-30) REVERT: E 47 ARG cc_start: 0.8790 (mtt90) cc_final: 0.8404 (mtt90) REVERT: G 496 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8448 (mptp) REVERT: G 546 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8886 (ttm) REVERT: G 859 ARG cc_start: 0.8428 (mtp85) cc_final: 0.8158 (mtp-110) REVERT: C 80 MET cc_start: 0.9066 (ttt) cc_final: 0.8843 (ttm) REVERT: C 105 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8860 (mm) REVERT: C 240 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: C 298 THR cc_start: 0.8919 (m) cc_final: 0.8609 (t) REVERT: C 597 ASP cc_start: 0.8643 (t0) cc_final: 0.8297 (t0) REVERT: B 13 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6940 (mm-30) REVERT: B 44 ASP cc_start: 0.8386 (m-30) cc_final: 0.8179 (m-30) REVERT: B 57 TYR cc_start: 0.8969 (t80) cc_final: 0.8692 (t80) REVERT: I 126 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8663 (mttm) REVERT: H 23 LEU cc_start: 0.8973 (mm) cc_final: 0.8747 (mt) REVERT: H 36 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: H 122 MET cc_start: 0.8784 (mmp) cc_final: 0.8352 (mmp) REVERT: H 228 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: H 242 TYR cc_start: 0.8821 (m-80) cc_final: 0.8401 (m-80) REVERT: A 79 ASP cc_start: 0.8362 (t0) cc_final: 0.8078 (t0) REVERT: A 134 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.5893 (ptt180) REVERT: L 1 MET cc_start: 0.8167 (tpp) cc_final: 0.7565 (mmm) REVERT: L 127 MET cc_start: 0.8615 (tpt) cc_final: 0.8258 (tpt) REVERT: L 571 ILE cc_start: 0.7794 (mt) cc_final: 0.7462 (mp) REVERT: M 20 THR cc_start: 0.8897 (p) cc_final: 0.8679 (p) REVERT: M 74 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7489 (tpt170) REVERT: M 122 TRP cc_start: 0.7236 (t-100) cc_final: 0.6308 (t60) REVERT: M 136 MET cc_start: 0.8885 (mmm) cc_final: 0.8583 (mmp) REVERT: M 185 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.9052 (ttm) REVERT: M 224 MET cc_start: 0.8472 (tmm) cc_final: 0.8004 (tmm) REVERT: M 235 MET cc_start: 0.9092 (tpp) cc_final: 0.8542 (ttm) REVERT: M 398 MET cc_start: 0.8718 (tpt) cc_final: 0.8469 (tpt) REVERT: N 219 SER cc_start: 0.8813 (m) cc_final: 0.8489 (p) REVERT: N 280 SER cc_start: 0.8646 (t) cc_final: 0.8050 (m) REVERT: K 26 ARG cc_start: 0.7693 (ttm-80) cc_final: 0.7477 (ttm110) REVERT: K 31 MET cc_start: 0.8469 (mtp) cc_final: 0.8257 (mtp) REVERT: K 87 ARG cc_start: 0.7749 (tmt90) cc_final: 0.7478 (tmt90) REVERT: J 91 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7872 (pp30) outliers start: 84 outliers final: 50 residues processed: 525 average time/residue: 0.6773 time to fit residues: 431.8581 Evaluate side-chains 522 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 458 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 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 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 670 GLN 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 45 MET 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 36 GLU Chi-restraints excluded: chain H residue 228 GLU 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 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 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 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 70 VAL 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: 3.9990 chunk 368 optimal weight: 9.9990 chunk 389 optimal weight: 6.9990 chunk 365 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 314 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 433 optimal weight: 5.9990 chunk 414 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 C 344 GLN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN H 323 GLN ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 335 GLN M 495 ASN M 502 ASN K 88 GLN J 75 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.084876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.067906 restraints weight = 53596.972| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.16 r_work: 0.2806 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1870 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= 0.416 Angle : 2.495 50.631 52670 Z= 1.432 Chirality : 0.443 6.495 5853 Planarity : 0.005 0.055 6571 Dihedral : 7.601 175.899 5569 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.16 % Allowed : 21.21 % Favored : 76.63 % 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: 0.81 (0.12), residues: 4728 helix: 1.39 (0.10), residues: 2680 sheet: -0.54 (0.29), residues: 321 loop : -0.53 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 804 TYR 0.019 0.002 TYR M 435 PHE 0.026 0.002 PHE L 341 TRP 0.019 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01181 / 0.42 (38762) covalent geometry : angle 2.18114 / 1.43 (52577) hydrogen bonds : bond 0.05247 / 3.47 ( 1700) hydrogen bonds : angle 4.21753 / 3.04 ( 5100) metal coordination : bond 0.03973 / 2.52 ( 36) metal coordination : angle 28.92418 / 20.28 ( 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 545 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 461 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: F 30 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8243 (mtm180) REVERT: F 182 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: G 496 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8507 (mptp) REVERT: G 874 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: C 80 MET cc_start: 0.9095 (ttt) cc_final: 0.8805 (ttm) REVERT: C 105 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8841 (mm) REVERT: C 194 MET cc_start: 0.8827 (mmt) cc_final: 0.8428 (mmt) REVERT: C 216 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7922 (ttt) REVERT: C 240 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7161 (tp30) REVERT: C 597 ASP cc_start: 0.8696 (t0) cc_final: 0.8313 (t0) REVERT: B 13 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7009 (mm-30) REVERT: B 44 ASP cc_start: 0.8400 (m-30) cc_final: 0.8186 (m-30) REVERT: I 126 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8684 (mttm) REVERT: H 23 LEU cc_start: 0.8969 (mm) cc_final: 0.8738 (mt) REVERT: H 36 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: H 122 MET cc_start: 0.8828 (mmp) cc_final: 0.8499 (mmp) REVERT: H 228 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: H 242 TYR cc_start: 0.8840 (m-80) cc_final: 0.8428 (m-80) REVERT: A 134 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.5871 (ptt180) REVERT: L 1 MET cc_start: 0.8216 (tpp) cc_final: 0.7718 (mmm) REVERT: L 571 ILE cc_start: 0.7782 (mt) cc_final: 0.7479 (mt) REVERT: M 74 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7423 (tpt170) REVERT: M 122 TRP cc_start: 0.7244 (t-100) cc_final: 0.6245 (t60) REVERT: M 136 MET cc_start: 0.8853 (mmm) cc_final: 0.8539 (mmp) REVERT: M 224 MET cc_start: 0.8459 (tmm) cc_final: 0.8008 (tmm) REVERT: M 235 MET cc_start: 0.9129 (tpp) cc_final: 0.8781 (ttm) REVERT: M 372 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7606 (mtm180) REVERT: M 374 MET cc_start: 0.8874 (ptt) cc_final: 0.8369 (ptt) REVERT: M 381 MET cc_start: 0.8388 (ptt) cc_final: 0.8138 (ptt) REVERT: M 398 MET cc_start: 0.8783 (tpt) cc_final: 0.8543 (tpt) REVERT: N 219 SER cc_start: 0.8847 (m) cc_final: 0.8522 (p) REVERT: N 280 SER cc_start: 0.8694 (t) cc_final: 0.8102 (m) REVERT: N 450 TYR cc_start: 0.8777 (t80) cc_final: 0.8523 (t80) REVERT: N 480 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8055 (mm) REVERT: K 26 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7506 (ttm110) REVERT: K 87 ARG cc_start: 0.7858 (tmt90) cc_final: 0.7236 (tmt90) REVERT: J 91 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7905 (pp30) outliers start: 84 outliers final: 50 residues processed: 514 average time/residue: 0.7406 time to fit residues: 462.0887 Evaluate side-chains 515 residues out of total 3896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 450 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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 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 223 MET 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 670 GLN 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 216 MET Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 272 THR 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 36 GLU Chi-restraints excluded: chain H residue 156 TYR Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 251 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 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 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 253 THR Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 426 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 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: 9.9990 chunk 115 optimal weight: 9.9990 chunk 352 optimal weight: 2.9990 chunk 456 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 chunk 332 optimal weight: 9.9990 chunk 421 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 283 optimal weight: 10.0000 chunk 329 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 159 ASN 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 312 ASN H 323 GLN M 502 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 = 0.3252 r_free = 0.3252 target = 0.085091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.068136 restraints weight = 53889.866| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.17 r_work: 0.2810 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1888 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= 0.408 Angle : 2.495 50.602 52670 Z= 1.432 Chirality : 0.443 6.478 5853 Planarity : 0.005 0.056 6571 Dihedral : 7.598 176.093 5567 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.19 % Allowed : 21.16 % Favored : 76.66 % 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: 0.80 (0.12), residues: 4728 helix: 1.39 (0.10), residues: 2677 sheet: -0.53 (0.29), residues: 321 loop : -0.55 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 804 TYR 0.019 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/Z covalent geometry : bond 0.01165 / 0.41 (38762) covalent geometry : angle 2.17981 / 1.43 (52577) hydrogen bonds : bond 0.05154 / 3.41 ( 1700) hydrogen bonds : angle 4.21521 / 3.04 ( 5100) metal coordination : bond 0.03671 / 2.32 ( 36) metal coordination : angle 28.95715 / 20.28 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14103.04 seconds wall clock time: 240 minutes 32.86 seconds (14432.86 seconds total)