Starting phenix.real_space_refine on Sat Mar 7 00:44:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p7k_13238/03_2026/7p7k_13238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p7k_13238/03_2026/7p7k_13238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p7k_13238/03_2026/7p7k_13238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p7k_13238/03_2026/7p7k_13238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p7k_13238/03_2026/7p7k_13238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p7k_13238/03_2026/7p7k_13238.map" } resolution = 3.1 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= 0.005 sd= 0.019 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 9 5.49 5 S 263 5.16 5 C 23789 2.51 5 N 6029 2.21 5 O 6408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.07s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36531 Number of models: 1 Model: "" Number of chains: 23 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: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4575 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 533} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1330 Classifications: {'peptide': 168} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 156} Chain breaks: 2 Chain: "I" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1185 Classifications: {'peptide': 149} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 135} Chain: "H" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2334 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 285} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "L" Number of atoms: 4548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4548 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 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: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3620 Classifications: {'peptide': 478} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 1 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1210 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 156} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "L" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 159 Unusual residues: {'3PE': 3, 'LFA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "M" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 70.538 58.904 201.172 1.00 28.99 S ATOM 2741 SG CYS F 357 74.005 58.437 205.554 1.00 43.17 S ATOM 3062 SG CYS F 398 68.353 54.803 205.881 1.00 42.91 S ATOM 2697 SG CYS F 351 72.964 52.636 202.267 1.00 37.56 S ATOM 4054 SG CYS E 92 81.619 50.445 221.840 1.00 59.56 S ATOM 4088 SG CYS E 97 81.816 51.160 225.339 1.00 68.83 S ATOM 4366 SG CYS E 133 76.505 49.633 221.578 1.00 71.18 S ATOM 4392 SG CYS E 137 75.627 50.243 224.764 1.00 65.94 S ATOM 5476 SG CYS G 114 80.757 65.791 183.843 1.00 24.10 S ATOM 5416 SG CYS G 105 85.811 69.990 185.414 1.00 29.22 S ATOM 5436 SG CYS G 108 86.771 64.122 182.991 1.00 25.62 S ATOM 5830 SG CYS G 156 75.340 57.687 188.612 1.00 21.94 S ATOM 5811 SG CYS G 153 81.237 56.857 191.543 1.00 22.70 S ATOM 5859 SG CYS G 159 78.620 52.186 187.920 1.00 19.92 S ATOM 6203 SG CYS G 203 80.491 57.535 184.915 1.00 12.85 S ATOM 6428 SG CYS G 230 77.580 49.451 163.675 1.00 19.08 S ATOM 6713 SG CYS G 265 77.761 45.572 168.945 1.00 19.36 S ATOM 6476 SG CYS G 237 72.273 48.795 166.730 1.00 17.83 S ATOM 6452 SG CYS G 233 74.822 43.606 163.652 1.00 19.24 S ATOM 4877 SG CYS G 36 68.883 58.298 191.250 1.00 24.33 S ATOM 4953 SG CYS G 47 70.340 61.611 191.813 1.00 22.94 S ATOM 4979 SG CYS G 50 64.438 63.051 191.738 1.00 34.28 S ATOM 5128 SG CYS G 69 64.164 59.419 191.183 1.00 29.03 S ATOM 16871 SG CYS B 129 89.711 94.343 160.263 1.00 39.78 S ATOM 16434 SG CYS B 64 94.680 98.365 162.055 1.00 64.15 S ATOM 16428 SG CYS B 63 89.031 99.912 164.071 1.00 62.31 S ATOM 17088 SG CYS B 158 91.632 94.189 166.081 1.00 71.00 S ATOM 18129 SG CYS I 102 90.348 88.169 172.013 1.00 17.46 S ATOM 18104 SG CYS I 99 95.978 87.161 168.467 1.00 11.91 S ATOM 18147 SG CYS I 105 94.601 83.745 173.771 1.00 28.17 S ATOM 17862 SG CYS I 70 90.800 82.960 168.579 1.00 15.21 S ATOM 18176 SG CYS I 109 95.943 78.155 180.014 1.00 17.05 S ATOM 17839 SG CYS I 66 94.015 77.502 173.877 1.00 12.17 S ATOM 17799 SG CYS I 60 98.342 73.416 175.968 1.00 21.62 S ATOM 17817 SG CYS I 63 92.113 73.453 178.604 1.00 10.39 S Time building chain proxies: 8.30, per 1000 atoms: 0.23 Number of scatterers: 36531 At special positions: 0 Unit cell: (154.76, 208.82, 252.28, 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 263 16.00 P 9 15.00 O 6408 8.00 N 6029 7.00 C 23789 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: 3.18 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="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="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" SF4 G1003 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " Number of angles added : 93 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8460 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 0 sheets defined 53.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 107 Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.709A pdb=" N ASP F 306 " --> pdb=" O GLU F 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 302 through 306' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 349 Processing helix chain 'F' and resid 355 through 373 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.518A pdb=" N SER E 36 " --> pdb=" O PRO E 32 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.059A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.788A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 276 removed outlier: 5.023A pdb=" N TYR G 272 " --> pdb=" O GLY G 268 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY G 273 " --> pdb=" O ARG G 269 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TYR G 274 " --> pdb=" O PHE G 270 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN G 276 " --> pdb=" O TYR G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 368 through 373 removed outlier: 4.403A pdb=" N GLU G 372 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER G 373 " --> pdb=" O ARG G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.549A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 424 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 605 removed outlier: 4.812A pdb=" N ASN G 605 " --> pdb=" O ALA G 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 605' Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 690 removed outlier: 5.348A pdb=" N GLY G 687 " --> pdb=" O PRO G 683 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE G 688 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS G 689 " --> pdb=" O LEU G 685 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASP G 690 " --> pdb=" O ALA G 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 683 through 690' Processing helix chain 'G' and resid 764 through 768 removed outlier: 5.175A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 768' Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 833 through 836 No H-bonds generated for 'chain 'G' and resid 833 through 836' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 65 removed outlier: 5.059A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 removed outlier: 5.384A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 326 Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 No H-bonds generated for 'chain 'I' and resid 127 through 130' Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' Processing helix chain 'H' and resid 6 through 39 Processing helix chain 'H' and resid 56 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.898A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 137 removed outlier: 4.716A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.025A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU H 160 " --> pdb=" O TYR H 156 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 231 through 257 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 322 removed outlier: 4.538A pdb=" N CYS H 305 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU H 306 " --> pdb=" O TRP H 302 " (cutoff:3.500A) Proline residue: H 307 - end of helix Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 89 Processing helix chain 'A' and resid 97 through 120 Processing helix chain 'L' and resid 4 through 20 removed outlier: 4.650A 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 131 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.433A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 256 removed outlier: 4.035A pdb=" N ALA L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 268 Processing helix chain 'L' and resid 270 through 273 No H-bonds generated for 'chain 'L' and resid 270 through 273' Processing helix chain 'L' and resid 277 through 298 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 436 Processing helix chain 'L' and resid 455 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 511 Processing helix chain 'L' and resid 517 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 560 removed outlier: 5.087A pdb=" N LYS L 551 " --> pdb=" O LYS L 547 " (cutoff:3.500A) Proline residue: L 552 - end of helix Processing helix chain 'L' and resid 564 through 584 Proline residue: L 572 - end of helix Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 28 through 49 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 145 Processing helix chain 'M' and resid 147 through 156 Processing helix chain 'M' and resid 165 through 199 Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 217 through 233 removed outlier: 6.266A pdb=" N TYR M 221 " --> pdb=" O SER M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 249 Processing helix chain 'M' and resid 256 through 262 removed outlier: 3.953A pdb=" N ILE M 262 " --> pdb=" O ASP M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 275 Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 396 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 501 removed outlier: 4.822A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 57 removed outlier: 4.496A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.224A 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: 4.204A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 180 Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.448A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 288 removed outlier: 4.046A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 320 through 347 removed outlier: 5.194A pdb=" N GLU N 324 " --> pdb=" O GLU N 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 479 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 111 removed outlier: 5.517A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1679 hydrogen bonds defined for protein. 5037 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: 5.80 Time building geometry restraints manager: 4.17 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: 15545 1.42 - 1.64: 21400 1.64 - 1.86: 401 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 37438 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.485 1.382 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C4A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 1.300 1.371 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" O5' FMN F 502 " pdb=" P FMN F 502 " ideal model delta sigma weight residual 1.676 1.606 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C10 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.443 1.381 0.062 2.00e-02 2.50e+03 9.65e+00 bond pdb=" O13 3PE H 602 " pdb=" P 3PE H 602 " ideal model delta sigma weight residual 1.654 1.592 0.062 2.00e-02 2.50e+03 9.52e+00 ... (remaining 37433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 50000 2.33 - 4.67: 672 4.67 - 7.00: 91 7.00 - 9.34: 25 9.34 - 11.67: 4 Bond angle restraints: 50792 Sorted by residual: angle pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta sigma weight residual 121.80 133.47 -11.67 2.44e+00 1.68e-01 2.29e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 99.59 10.22 2.21e+00 2.05e-01 2.14e+01 angle pdb=" C ALA G 177 " pdb=" N HIS G 178 " pdb=" CA HIS G 178 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.08e+01 angle pdb=" S3 SF4 F 501 " pdb="FE1 SF4 F 501 " pdb=" S4 SF4 F 501 " ideal model delta sigma weight residual 104.10 110.14 -6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" N MET C 387 " pdb=" CA MET C 387 " pdb=" C MET C 387 " ideal model delta sigma weight residual 109.81 118.71 -8.90 2.21e+00 2.05e-01 1.62e+01 ... (remaining 50787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 21040 23.20 - 46.40: 826 46.40 - 69.60: 135 69.60 - 92.80: 21 92.80 - 116.01: 6 Dihedral angle restraints: 22028 sinusoidal: 8804 harmonic: 13224 Sorted by residual: dihedral pdb=" CA HIS H 210 " pdb=" C HIS H 210 " pdb=" N PRO H 211 " pdb=" CA PRO H 211 " ideal model delta harmonic sigma weight residual 180.00 130.20 49.80 0 5.00e+00 4.00e-02 9.92e+01 dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 135.99 44.01 0 5.00e+00 4.00e-02 7.75e+01 dihedral pdb=" CA ASN G 260 " pdb=" C ASN G 260 " pdb=" N HIS G 261 " pdb=" CA HIS G 261 " ideal model delta harmonic sigma weight residual 180.00 -144.85 -35.15 0 5.00e+00 4.00e-02 4.94e+01 ... (remaining 22025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.236: 5655 4.236 - 8.471: 0 8.471 - 12.707: 0 12.707 - 16.942: 0 16.942 - 21.178: 28 Chirality restraints: 5683 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 -21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.60 21.16 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 -10.60 21.15 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5680 not shown) Planarity restraints: 6350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C VAL N 63 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.024 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS H 210 " 0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO H 211 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO H 211 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 211 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 212 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO F 213 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO F 213 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 213 " 0.040 5.00e-02 4.00e+02 ... (remaining 6347 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7366 2.77 - 3.30: 34489 3.30 - 3.84: 66387 3.84 - 4.37: 80453 4.37 - 4.90: 135242 Nonbonded interactions: 323937 Sorted by model distance: nonbonded pdb=" OG1 THR I 82 " pdb=" OD1 ASP I 84 " model vdw 2.238 3.040 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.248 3.040 nonbonded pdb=" OE2 GLU N 324 " pdb=" OH TYR N 397 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR G 255 " pdb=" O GLY G 776 " model vdw 2.272 3.040 ... (remaining 323932 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 35.620 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 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 : 0.006 0.238 37474 Z= 0.270 Angle : 0.737 15.224 50885 Z= 0.375 Chirality : 1.482 21.178 5683 Planarity : 0.006 0.085 6350 Dihedral : 12.967 116.006 13568 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.51 % Favored : 97.47 % Rotamer: Outliers : 2.21 % Allowed : 5.64 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.11), residues: 4584 helix: 0.28 (0.09), residues: 2660 sheet: -0.66 (0.28), residues: 302 loop : -0.98 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 219 TYR 0.031 0.002 TYR L 428 PHE 0.041 0.002 PHE L 341 TRP 0.032 0.002 TRP M 47 HIS 0.009 0.001 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00616 (37438) covalent geometry : angle 0.71502 (50792) hydrogen bonds : bond 0.06097 ( 1679) hydrogen bonds : angle 4.68356 ( 5037) metal coordination : bond 0.06212 ( 36) metal coordination : angle 4.26977 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 603 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 158 LYS cc_start: 0.9040 (mptt) cc_final: 0.8839 (mmtm) REVERT: F 238 ASN cc_start: 0.8863 (m-40) cc_final: 0.8595 (m-40) REVERT: F 250 MET cc_start: 0.9154 (mtt) cc_final: 0.8942 (mtt) REVERT: F 387 LEU cc_start: 0.9165 (tp) cc_final: 0.8852 (mt) REVERT: E 19 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8568 (ttp-170) REVERT: E 112 LYS cc_start: 0.8440 (tptm) cc_final: 0.8220 (tptt) REVERT: E 114 ASN cc_start: 0.9094 (t0) cc_final: 0.8878 (t0) REVERT: G 233 CYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8371 (p) REVERT: G 405 GLU cc_start: 0.8850 (tt0) cc_final: 0.8567 (pt0) REVERT: G 854 VAL cc_start: 0.8813 (t) cc_final: 0.8552 (m) REVERT: G 862 PHE cc_start: 0.9271 (p90) cc_final: 0.9006 (p90) REVERT: G 896 VAL cc_start: 0.9240 (p) cc_final: 0.8915 (m) REVERT: G 901 HIS cc_start: 0.8490 (p90) cc_final: 0.8062 (p-80) REVERT: C 36 ASP cc_start: 0.8777 (p0) cc_final: 0.8510 (p0) REVERT: C 204 TRP cc_start: 0.8439 (m100) cc_final: 0.8190 (m100) REVERT: C 595 MET cc_start: 0.9224 (tpt) cc_final: 0.8975 (mmm) REVERT: I 55 ASP cc_start: 0.8718 (m-30) cc_final: 0.8372 (m-30) REVERT: I 147 GLU cc_start: 0.8862 (mp0) cc_final: 0.8248 (pp20) REVERT: I 153 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.6714 (mmt) REVERT: H 27 THR cc_start: 0.8606 (m) cc_final: 0.8364 (p) REVERT: H 37 ARG cc_start: 0.7678 (ttm170) cc_final: 0.7313 (ttt180) REVERT: H 152 GLN cc_start: 0.8623 (tt0) cc_final: 0.8380 (tt0) REVERT: H 229 TYR cc_start: 0.8464 (m-80) cc_final: 0.7996 (m-80) REVERT: H 285 ILE cc_start: 0.9050 (mm) cc_final: 0.8819 (mm) REVERT: H 296 GLN cc_start: 0.8784 (mt0) cc_final: 0.8505 (mt0) REVERT: H 298 MET cc_start: 0.8728 (mmp) cc_final: 0.8455 (mmp) REVERT: L 77 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: L 105 TRP cc_start: 0.8350 (t60) cc_final: 0.7508 (m100) REVERT: L 365 MET cc_start: 0.7868 (mpp) cc_final: 0.7103 (mtm) REVERT: L 424 MET cc_start: 0.8535 (mtp) cc_final: 0.8333 (mtm) REVERT: M 20 THR cc_start: 0.9137 (t) cc_final: 0.8921 (t) REVERT: M 224 MET cc_start: 0.8999 (tmm) cc_final: 0.8465 (tmm) REVERT: M 291 MET cc_start: 0.9019 (mtm) cc_final: 0.8794 (mtm) REVERT: N 1 MET cc_start: 0.6935 (mtp) cc_final: 0.5622 (ttp) REVERT: N 72 PHE cc_start: 0.9065 (t80) cc_final: 0.8847 (t80) REVERT: K 99 ARG cc_start: 0.8176 (ptp-170) cc_final: 0.7941 (ptp90) REVERT: J 55 GLU cc_start: 0.9003 (tp30) cc_final: 0.8680 (tp30) outliers start: 83 outliers final: 26 residues processed: 660 average time/residue: 0.2346 time to fit residues: 247.1290 Evaluate side-chains 498 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 469 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 233 CYS Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain J residue 23 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 HIS F 22 GLN F 53 GLN F 237 GLN F 304 HIS F 425 GLN E 44 GLN E 106 GLN G 20 ASN G 238 ASN G 583 ASN G 808 GLN G 883 GLN C 101 HIS C 283 ASN C 359 HIS B 47 ASN N 404 GLN K 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.078050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.057831 restraints weight = 59597.662| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 1.48 r_work: 0.2596 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 37474 Z= 0.419 Angle : 2.530 58.118 50885 Z= 1.453 Chirality : 0.453 6.592 5683 Planarity : 0.005 0.068 6350 Dihedral : 8.909 111.847 5488 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.31 % Favored : 97.67 % Rotamer: Outliers : 1.81 % Allowed : 8.17 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.12), residues: 4584 helix: 1.06 (0.10), residues: 2651 sheet: -0.42 (0.30), residues: 296 loop : -0.79 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 274 TYR 0.023 0.002 TYR L 428 PHE 0.028 0.002 PHE L 341 TRP 0.028 0.001 TRP M 47 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01179 (37438) covalent geometry : angle 2.20700 (50792) hydrogen bonds : bond 0.05337 ( 1679) hydrogen bonds : angle 4.27767 ( 5037) metal coordination : bond 0.04985 ( 36) metal coordination : angle 29.03730 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 490 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: F 250 MET cc_start: 0.9036 (mtt) cc_final: 0.8829 (mtt) REVERT: E 114 ASN cc_start: 0.8980 (t0) cc_final: 0.8645 (t0) REVERT: G 56 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8492 (mm-40) REVERT: G 901 HIS cc_start: 0.8229 (p90) cc_final: 0.7908 (p-80) REVERT: C 36 ASP cc_start: 0.8339 (p0) cc_final: 0.8131 (p0) REVERT: C 243 VAL cc_start: 0.9171 (OUTLIER) cc_final: 0.8910 (p) REVERT: C 597 ASP cc_start: 0.8559 (t0) cc_final: 0.8230 (t0) REVERT: I 147 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: H 152 GLN cc_start: 0.8661 (tt0) cc_final: 0.8397 (tt0) REVERT: H 229 TYR cc_start: 0.8349 (m-80) cc_final: 0.7792 (m-80) REVERT: H 285 ILE cc_start: 0.9041 (mm) cc_final: 0.8814 (mm) REVERT: H 298 MET cc_start: 0.8822 (mmp) cc_final: 0.8610 (mmp) REVERT: H 322 TRP cc_start: 0.8037 (t60) cc_final: 0.7738 (t-100) REVERT: L 150 SER cc_start: 0.9336 (t) cc_final: 0.8933 (m) REVERT: L 315 GLN cc_start: 0.8956 (mm110) cc_final: 0.8733 (mm-40) REVERT: M 152 PHE cc_start: 0.8212 (m-10) cc_final: 0.7974 (m-10) REVERT: M 224 MET cc_start: 0.8884 (tmm) cc_final: 0.8134 (tmm) REVERT: M 373 MET cc_start: 0.8764 (mmm) cc_final: 0.8503 (mmm) REVERT: N 1 MET cc_start: 0.7045 (mtp) cc_final: 0.5837 (ttp) REVERT: J 1 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7490 (ttm) REVERT: J 72 MET cc_start: 0.8320 (mmt) cc_final: 0.8116 (mmt) REVERT: J 94 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8578 (mm) outliers start: 68 outliers final: 42 residues processed: 542 average time/residue: 0.2251 time to fit residues: 197.4020 Evaluate side-chains 502 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 455 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 261 HIS Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 263 LEU 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 64 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 112 optimal weight: 10.0000 chunk 450 optimal weight: 7.9990 chunk 307 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 319 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 chunk 452 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 422 optimal weight: 0.6980 chunk 313 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 304 HIS F 425 GLN E 106 GLN G 238 ASN C 409 GLN B 47 ASN H 296 GLN ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 232 GLN N 317 GLN N 404 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.058256 restraints weight = 59239.540| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 1.40 r_work: 0.2607 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 37474 Z= 0.407 Angle : 2.522 57.754 50885 Z= 1.450 Chirality : 0.449 6.512 5683 Planarity : 0.004 0.067 6350 Dihedral : 8.679 112.424 5470 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.31 % Favored : 97.67 % Rotamer: Outliers : 2.23 % Allowed : 8.62 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.12), residues: 4584 helix: 1.38 (0.10), residues: 2654 sheet: -0.35 (0.30), residues: 298 loop : -0.67 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 664 TYR 0.025 0.002 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.024 0.001 TRP M 47 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01168 (37438) covalent geometry : angle 2.19808 (50792) hydrogen bonds : bond 0.05009 ( 1679) hydrogen bonds : angle 4.16646 ( 5037) metal coordination : bond 0.04249 ( 36) metal coordination : angle 28.99179 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 468 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: F 250 MET cc_start: 0.9036 (mtt) cc_final: 0.8812 (mtt) REVERT: G 215 GLU cc_start: 0.8211 (tp30) cc_final: 0.7993 (tp30) REVERT: G 617 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: G 901 HIS cc_start: 0.8211 (p90) cc_final: 0.7854 (p-80) REVERT: C 597 ASP cc_start: 0.8519 (t0) cc_final: 0.8284 (t0) REVERT: B 170 MET cc_start: 0.8593 (mmt) cc_final: 0.8372 (mmt) REVERT: I 147 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: I 153 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7090 (mmt) REVERT: H 152 GLN cc_start: 0.8615 (tt0) cc_final: 0.8375 (tt0) REVERT: H 229 TYR cc_start: 0.8358 (m-80) cc_final: 0.7806 (m-80) REVERT: H 285 ILE cc_start: 0.9007 (mm) cc_final: 0.8800 (mm) REVERT: H 298 MET cc_start: 0.8769 (mmp) cc_final: 0.8556 (mmp) REVERT: H 322 TRP cc_start: 0.8081 (t60) cc_final: 0.7800 (t-100) REVERT: M 152 PHE cc_start: 0.8118 (m-10) cc_final: 0.7903 (m-10) REVERT: M 224 MET cc_start: 0.8872 (tmm) cc_final: 0.8138 (tmm) REVERT: M 373 MET cc_start: 0.8789 (mmm) cc_final: 0.8537 (mmm) REVERT: N 1 MET cc_start: 0.7043 (mtp) cc_final: 0.5852 (ttp) REVERT: J 94 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8597 (mm) REVERT: J 116 ASP cc_start: 0.8609 (t70) cc_final: 0.8395 (t0) outliers start: 84 outliers final: 53 residues processed: 532 average time/residue: 0.2243 time to fit residues: 193.9361 Evaluate side-chains 507 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 450 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 261 HIS Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 223 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 267 optimal weight: 40.0000 chunk 363 optimal weight: 0.5980 chunk 392 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 340 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 453 optimal weight: 0.8980 chunk 319 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 304 HIS F 425 GLN E 106 GLN B 47 ASN H 261 GLN H 296 GLN H 312 ASN ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 149 GLN N 317 GLN N 404 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.080223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.060597 restraints weight = 59244.886| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.45 r_work: 0.2672 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 37474 Z= 0.387 Angle : 2.516 56.178 50885 Z= 1.447 Chirality : 0.445 6.396 5683 Planarity : 0.004 0.067 6350 Dihedral : 8.342 110.824 5469 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.10 % Allowed : 9.10 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.12), residues: 4584 helix: 1.67 (0.10), residues: 2647 sheet: -0.27 (0.30), residues: 299 loop : -0.56 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 374 TYR 0.027 0.001 TYR M 435 PHE 0.028 0.001 PHE L 341 TRP 0.023 0.001 TRP M 47 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01136 (37438) covalent geometry : angle 2.18828 (50792) hydrogen bonds : bond 0.04208 ( 1679) hydrogen bonds : angle 3.93656 ( 5037) metal coordination : bond 0.02625 ( 36) metal coordination : angle 29.14407 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 488 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 MET cc_start: 0.9049 (mmm) cc_final: 0.8832 (mmm) REVERT: F 250 MET cc_start: 0.9028 (mtt) cc_final: 0.8786 (mtt) REVERT: E 114 ASN cc_start: 0.8850 (t0) cc_final: 0.8617 (t0) REVERT: G 215 GLU cc_start: 0.8233 (tp30) cc_final: 0.8009 (tp30) REVERT: G 617 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: G 890 MET cc_start: 0.8331 (mmm) cc_final: 0.8010 (mmt) REVERT: G 901 HIS cc_start: 0.8139 (p90) cc_final: 0.7818 (p-80) REVERT: C 597 ASP cc_start: 0.8466 (t0) cc_final: 0.8224 (t0) REVERT: I 153 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.6930 (mmt) REVERT: H 152 GLN cc_start: 0.8604 (tt0) cc_final: 0.8398 (tt0) REVERT: H 296 GLN cc_start: 0.8574 (mt0) cc_final: 0.8271 (mt0) REVERT: H 322 TRP cc_start: 0.8046 (t60) cc_final: 0.7745 (t-100) REVERT: M 224 MET cc_start: 0.8797 (tmm) cc_final: 0.8079 (tmm) REVERT: M 374 MET cc_start: 0.8712 (mtm) cc_final: 0.8499 (mtm) REVERT: M 429 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7911 (tt) REVERT: N 1 MET cc_start: 0.7061 (mtp) cc_final: 0.5880 (ttp) REVERT: N 63 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8333 (p) REVERT: J 6 TYR cc_start: 0.8881 (m-80) cc_final: 0.8579 (m-80) REVERT: J 116 ASP cc_start: 0.8371 (t70) cc_final: 0.8145 (t0) REVERT: J 117 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8326 (mm-40) outliers start: 79 outliers final: 44 residues processed: 545 average time/residue: 0.2291 time to fit residues: 200.7909 Evaluate side-chains 502 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 454 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 148 ASP 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 617 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 491 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 2 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 360 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 217 optimal weight: 20.0000 chunk 443 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 57 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN F 237 GLN F 304 HIS F 425 GLN E 106 GLN G 224 GLN G 352 GLN G 490 GLN G 808 GLN B 47 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 149 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN J 115 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.077021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.056845 restraints weight = 58987.897| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 1.47 r_work: 0.2572 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 37474 Z= 0.446 Angle : 2.532 54.146 50885 Z= 1.455 Chirality : 0.452 6.564 5683 Planarity : 0.005 0.065 6350 Dihedral : 8.620 114.344 5458 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.55 % Favored : 97.43 % Rotamer: Outliers : 2.10 % Allowed : 9.50 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.12), residues: 4584 helix: 1.55 (0.10), residues: 2659 sheet: -0.41 (0.29), residues: 310 loop : -0.51 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 274 TYR 0.021 0.002 TYR H 242 PHE 0.025 0.002 PHE L 341 TRP 0.025 0.001 TRP M 47 HIS 0.008 0.001 HIS G 261 Details of bonding type rmsd covalent geometry : bond 0.01239 (37438) covalent geometry : angle 2.21210 (50792) hydrogen bonds : bond 0.05529 ( 1679) hydrogen bonds : angle 4.20946 ( 5037) metal coordination : bond 0.04811 ( 36) metal coordination : angle 28.91880 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 462 time to evaluate : 1.109 Fit side-chains REVERT: F 250 MET cc_start: 0.9065 (mtt) cc_final: 0.8839 (mtt) REVERT: E 114 ASN cc_start: 0.8995 (t0) cc_final: 0.8723 (t0) REVERT: G 562 ARG cc_start: 0.9006 (mtm-85) cc_final: 0.8657 (mtm-85) REVERT: G 617 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: B 135 MET cc_start: 0.8845 (ptm) cc_final: 0.8604 (ptm) REVERT: I 153 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7075 (mmt) REVERT: H 152 GLN cc_start: 0.8614 (tt0) cc_final: 0.8371 (tt0) REVERT: H 322 TRP cc_start: 0.8154 (t60) cc_final: 0.7833 (t-100) REVERT: L 407 MET cc_start: 0.8589 (tpp) cc_final: 0.8171 (tpp) REVERT: L 415 MET cc_start: 0.8223 (tmm) cc_final: 0.7850 (tmm) REVERT: M 224 MET cc_start: 0.8847 (tmm) cc_final: 0.8057 (tmm) REVERT: M 429 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8112 (tt) REVERT: M 447 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8487 (mmtm) REVERT: N 1 MET cc_start: 0.7141 (mtp) cc_final: 0.6018 (ttp) REVERT: J 116 ASP cc_start: 0.8402 (t70) cc_final: 0.8136 (t0) outliers start: 79 outliers final: 61 residues processed: 520 average time/residue: 0.2358 time to fit residues: 197.0838 Evaluate side-chains 512 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 448 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 47 TRP Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 259 LEU 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 M residue 429 LEU Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 295 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 232 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 333 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 375 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 304 HIS F 425 GLN E 106 GLN G 490 GLN G 901 HIS B 47 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 HIS N 149 GLN N 232 GLN N 317 GLN N 404 GLN K 82 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.079020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.059016 restraints weight = 59128.787| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 1.47 r_work: 0.2628 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 37474 Z= 0.391 Angle : 2.518 55.260 50885 Z= 1.448 Chirality : 0.447 6.456 5683 Planarity : 0.004 0.067 6350 Dihedral : 8.374 111.864 5454 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.02 % Allowed : 9.71 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.12), residues: 4584 helix: 1.72 (0.10), residues: 2647 sheet: -0.35 (0.30), residues: 309 loop : -0.43 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 804 TYR 0.024 0.001 TYR N 424 PHE 0.027 0.001 PHE L 341 TRP 0.026 0.001 TRP M 47 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01142 (37438) covalent geometry : angle 2.19249 (50792) hydrogen bonds : bond 0.04572 ( 1679) hydrogen bonds : angle 4.01418 ( 5037) metal coordination : bond 0.03161 ( 36) metal coordination : angle 29.05916 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 460 time to evaluate : 1.301 Fit side-chains REVERT: F 250 MET cc_start: 0.9028 (mtt) cc_final: 0.8774 (mtt) REVERT: E 114 ASN cc_start: 0.8871 (t0) cc_final: 0.8608 (t0) REVERT: G 617 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: C 469 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9092 (mp) REVERT: C 597 ASP cc_start: 0.8417 (t0) cc_final: 0.8025 (t70) REVERT: I 153 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7013 (mmt) REVERT: H 152 GLN cc_start: 0.8635 (tt0) cc_final: 0.8434 (tt0) REVERT: H 268 PHE cc_start: 0.7888 (t80) cc_final: 0.7664 (t80) REVERT: H 322 TRP cc_start: 0.8123 (t60) cc_final: 0.7790 (t-100) REVERT: L 407 MET cc_start: 0.8557 (tpp) cc_final: 0.8060 (tpp) REVERT: L 415 MET cc_start: 0.8142 (tmm) cc_final: 0.7802 (tmm) REVERT: M 146 MET cc_start: 0.8340 (ptt) cc_final: 0.7800 (ptt) REVERT: M 224 MET cc_start: 0.8842 (tmm) cc_final: 0.8153 (tmm) REVERT: M 429 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7904 (tt) REVERT: N 1 MET cc_start: 0.7086 (mtp) cc_final: 0.5862 (ttp) REVERT: N 63 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8345 (p) outliers start: 76 outliers final: 58 residues processed: 517 average time/residue: 0.2276 time to fit residues: 191.5125 Evaluate side-chains 508 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 445 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 47 TRP Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 205 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 63 optimal weight: 0.0770 chunk 290 optimal weight: 8.9990 chunk 453 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 446 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 238 optimal weight: 30.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 304 HIS F 425 GLN E 106 GLN G 901 HIS B 47 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 317 GLN J 115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.078416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.058381 restraints weight = 59213.183| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 1.45 r_work: 0.2610 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 37474 Z= 0.401 Angle : 2.520 54.175 50885 Z= 1.449 Chirality : 0.448 6.476 5683 Planarity : 0.004 0.066 6350 Dihedral : 8.398 112.599 5454 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.31 % Favored : 97.67 % Rotamer: Outliers : 2.21 % Allowed : 9.95 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.12), residues: 4584 helix: 1.73 (0.10), residues: 2655 sheet: -0.36 (0.30), residues: 307 loop : -0.44 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 664 TYR 0.020 0.001 TYR N 424 PHE 0.025 0.001 PHE L 341 TRP 0.025 0.001 TRP M 47 HIS 0.008 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.01158 (37438) covalent geometry : angle 2.19613 (50792) hydrogen bonds : bond 0.04781 ( 1679) hydrogen bonds : angle 4.03798 ( 5037) metal coordination : bond 0.03617 ( 36) metal coordination : angle 28.97740 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 458 time to evaluate : 1.334 Fit side-chains REVERT: F 250 MET cc_start: 0.9036 (mtt) cc_final: 0.8788 (mtt) REVERT: E 114 ASN cc_start: 0.8887 (t0) cc_final: 0.8613 (t0) REVERT: G 562 ARG cc_start: 0.8983 (mtm-85) cc_final: 0.8583 (mtm-85) REVERT: G 617 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: C 469 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9118 (mp) REVERT: C 597 ASP cc_start: 0.8478 (t0) cc_final: 0.8147 (t70) REVERT: I 153 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7024 (mmt) REVERT: H 32 MET cc_start: 0.4667 (mtt) cc_final: 0.4044 (mtt) REVERT: H 147 MET cc_start: 0.7815 (mmt) cc_final: 0.7604 (mmt) REVERT: H 152 GLN cc_start: 0.8655 (tt0) cc_final: 0.8443 (tt0) REVERT: H 322 TRP cc_start: 0.8131 (t60) cc_final: 0.7825 (t-100) REVERT: M 224 MET cc_start: 0.8861 (tmm) cc_final: 0.8183 (tmm) REVERT: M 429 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7942 (tt) REVERT: N 1 MET cc_start: 0.7116 (mtp) cc_final: 0.5902 (ttp) REVERT: N 63 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8295 (p) REVERT: J 72 MET cc_start: 0.8281 (mmt) cc_final: 0.8075 (mmp) outliers start: 83 outliers final: 65 residues processed: 517 average time/residue: 0.2305 time to fit residues: 193.1191 Evaluate side-chains 521 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 451 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 47 TRP Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 406 optimal weight: 7.9990 chunk 274 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 367 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 304 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN G 828 GLN C 568 HIS B 47 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 GLN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS H 296 GLN ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 ASN N 7 ASN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.076423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.056142 restraints weight = 59117.000| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 1.47 r_work: 0.2555 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2422 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.239 37474 Z= 0.469 Angle : 2.540 53.071 50885 Z= 1.459 Chirality : 0.453 6.598 5683 Planarity : 0.005 0.078 6350 Dihedral : 8.800 114.878 5454 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 2.21 % Allowed : 10.00 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.12), residues: 4584 helix: 1.50 (0.10), residues: 2666 sheet: -0.60 (0.29), residues: 317 loop : -0.47 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 274 TYR 0.025 0.002 TYR H 242 PHE 0.024 0.002 PHE L 341 TRP 0.025 0.002 TRP M 47 HIS 0.008 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.01282 (37438) covalent geometry : angle 2.22116 (50792) hydrogen bonds : bond 0.05855 ( 1679) hydrogen bonds : angle 4.30615 ( 5037) metal coordination : bond 0.05091 ( 36) metal coordination : angle 28.92287 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 448 time to evaluate : 1.330 Fit side-chains REVERT: F 250 MET cc_start: 0.9087 (mtt) cc_final: 0.8855 (mtt) REVERT: E 114 ASN cc_start: 0.8945 (t0) cc_final: 0.8679 (t0) REVERT: G 562 ARG cc_start: 0.9014 (mtm-85) cc_final: 0.8634 (mtm-85) REVERT: G 617 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: C 469 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9158 (mp) REVERT: C 597 ASP cc_start: 0.8461 (t0) cc_final: 0.8185 (t0) REVERT: I 153 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7058 (mmt) REVERT: H 152 GLN cc_start: 0.8681 (tt0) cc_final: 0.8453 (tt0) REVERT: H 322 TRP cc_start: 0.8188 (t60) cc_final: 0.7854 (t-100) REVERT: M 224 MET cc_start: 0.8877 (tmm) cc_final: 0.8067 (tmm) REVERT: M 429 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8121 (tt) REVERT: N 1 MET cc_start: 0.7111 (mtp) cc_final: 0.6032 (ttp) REVERT: J 1 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7314 (ttm) outliers start: 83 outliers final: 64 residues processed: 505 average time/residue: 0.2331 time to fit residues: 189.0917 Evaluate side-chains 510 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 441 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 837 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 323 GLN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 47 TRP Chi-restraints excluded: chain M residue 233 VAL 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 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 72 GLU Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 101 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 280 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 336 optimal weight: 5.9990 chunk 378 optimal weight: 4.9990 chunk 448 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 243 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 237 GLN F 304 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN G 583 ASN C 568 HIS B 43 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 232 GLN N 317 GLN J 24 ASN J 115 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.077966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.057829 restraints weight = 58966.336| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 1.49 r_work: 0.2597 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 37474 Z= 0.403 Angle : 2.526 54.318 50885 Z= 1.452 Chirality : 0.448 6.473 5683 Planarity : 0.004 0.073 6350 Dihedral : 8.611 113.265 5454 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.23 % Favored : 97.75 % Rotamer: Outliers : 2.00 % Allowed : 10.30 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.12), residues: 4584 helix: 1.66 (0.10), residues: 2658 sheet: -0.51 (0.29), residues: 315 loop : -0.42 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 209 TYR 0.022 0.002 TYR H 242 PHE 0.026 0.001 PHE L 341 TRP 0.026 0.001 TRP M 47 HIS 0.009 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.01162 (37438) covalent geometry : angle 2.20206 (50792) hydrogen bonds : bond 0.04963 ( 1679) hydrogen bonds : angle 4.13582 ( 5037) metal coordination : bond 0.03651 ( 36) metal coordination : angle 29.01916 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 456 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: F 250 MET cc_start: 0.9065 (mtt) cc_final: 0.8816 (mtt) REVERT: E 114 ASN cc_start: 0.8935 (t0) cc_final: 0.8682 (t0) REVERT: G 215 GLU cc_start: 0.8420 (tp30) cc_final: 0.8213 (tp30) REVERT: G 562 ARG cc_start: 0.8988 (mtm-85) cc_final: 0.8587 (mtm-85) REVERT: G 617 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: C 469 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9117 (mp) REVERT: C 597 ASP cc_start: 0.8457 (t0) cc_final: 0.8195 (t0) REVERT: I 153 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7028 (mmt) REVERT: H 59 GLN cc_start: 0.8814 (tm-30) cc_final: 0.7584 (mm-40) REVERT: H 147 MET cc_start: 0.7986 (mmt) cc_final: 0.7785 (mmt) REVERT: H 152 GLN cc_start: 0.8671 (tt0) cc_final: 0.8449 (tt0) REVERT: H 209 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7696 (mmm160) REVERT: H 284 LEU cc_start: 0.8902 (mm) cc_final: 0.8702 (mt) REVERT: H 322 TRP cc_start: 0.8166 (t60) cc_final: 0.7833 (t-100) REVERT: M 224 MET cc_start: 0.8885 (tmm) cc_final: 0.8160 (tmm) REVERT: M 429 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7951 (tt) REVERT: N 1 MET cc_start: 0.7042 (mtp) cc_final: 0.5994 (ttp) REVERT: N 63 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8337 (p) outliers start: 75 outliers final: 60 residues processed: 510 average time/residue: 0.2279 time to fit residues: 188.3753 Evaluate side-chains 514 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 449 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 47 TRP Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 262 ILE Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 102 optimal weight: 0.0170 chunk 121 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 406 optimal weight: 3.9990 chunk 337 optimal weight: 0.9980 chunk 392 optimal weight: 2.9990 chunk 264 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 413 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 304 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN G 583 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 GLN ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 232 GLN N 317 GLN J 24 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.079033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.059102 restraints weight = 59089.488| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 1.45 r_work: 0.2629 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 37474 Z= 0.392 Angle : 2.522 54.180 50885 Z= 1.450 Chirality : 0.446 6.440 5683 Planarity : 0.004 0.071 6350 Dihedral : 8.434 112.398 5454 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.92 % Allowed : 10.48 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.12), residues: 4584 helix: 1.77 (0.10), residues: 2650 sheet: -0.51 (0.29), residues: 319 loop : -0.33 (0.16), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 804 TYR 0.025 0.001 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.027 0.001 TRP M 47 HIS 0.010 0.001 HIS G 901 Details of bonding type rmsd covalent geometry : bond 0.01145 (37438) covalent geometry : angle 2.19637 (50792) hydrogen bonds : bond 0.04598 ( 1679) hydrogen bonds : angle 4.03039 ( 5037) metal coordination : bond 0.03071 ( 36) metal coordination : angle 29.05764 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9168 Ramachandran restraints generated. 4584 Oldfield, 0 Emsley, 4584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 460 time to evaluate : 1.123 Fit side-chains REVERT: F 250 MET cc_start: 0.9069 (mtt) cc_final: 0.8819 (mtt) REVERT: E 114 ASN cc_start: 0.8922 (t0) cc_final: 0.8693 (t0) REVERT: G 215 GLU cc_start: 0.8407 (tp30) cc_final: 0.8199 (tp30) REVERT: G 617 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: C 469 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9117 (mp) REVERT: C 597 ASP cc_start: 0.8453 (t0) cc_final: 0.8209 (t0) REVERT: B 45 MET cc_start: 0.7726 (mmt) cc_final: 0.7350 (mmm) REVERT: I 153 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7019 (mmt) REVERT: H 152 GLN cc_start: 0.8653 (tt0) cc_final: 0.8433 (tt0) REVERT: H 209 ARG cc_start: 0.7883 (mmm160) cc_final: 0.7456 (mmm160) REVERT: H 213 ASP cc_start: 0.5806 (t0) cc_final: 0.5596 (t0) REVERT: H 322 TRP cc_start: 0.8159 (t60) cc_final: 0.7829 (t-100) REVERT: A 30 MET cc_start: 0.7453 (ttt) cc_final: 0.7050 (ttt) REVERT: M 224 MET cc_start: 0.8851 (tmm) cc_final: 0.8122 (tmm) REVERT: M 429 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7881 (tt) REVERT: N 1 MET cc_start: 0.7041 (mtp) cc_final: 0.5998 (ttp) REVERT: N 63 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8163 (p) REVERT: N 321 MET cc_start: 0.7497 (ptp) cc_final: 0.7248 (ptp) REVERT: J 6 TYR cc_start: 0.8966 (m-80) cc_final: 0.8666 (m-80) REVERT: J 64 MET cc_start: 0.8864 (mmp) cc_final: 0.8558 (mmp) REVERT: J 72 MET cc_start: 0.8294 (mmt) cc_final: 0.8040 (mmt) outliers start: 72 outliers final: 58 residues processed: 513 average time/residue: 0.2308 time to fit residues: 191.1208 Evaluate side-chains 516 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 453 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 611 SER Chi-restraints excluded: chain G residue 617 GLU Chi-restraints excluded: chain G residue 666 VAL Chi-restraints excluded: chain G residue 681 LYS Chi-restraints excluded: chain G residue 721 ILE Chi-restraints excluded: chain G residue 750 ARG Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 47 TRP Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 429 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 482 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 365 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 283 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 358 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 304 HIS ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN C 568 HIS ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS H 296 GLN ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 232 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.077369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.057160 restraints weight = 58608.937| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 1.47 r_work: 0.2579 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 37474 Z= 0.431 Angle : 2.533 53.313 50885 Z= 1.455 Chirality : 0.451 6.544 5683 Planarity : 0.005 0.069 6350 Dihedral : 8.665 113.584 5454 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.60 % Favored : 97.38 % Rotamer: Outliers : 1.97 % Allowed : 10.22 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.12), residues: 4584 helix: 1.63 (0.10), residues: 2665 sheet: -0.50 (0.29), residues: 317 loop : -0.40 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 804 TYR 0.023 0.002 TYR H 242 PHE 0.025 0.002 PHE L 341 TRP 0.026 0.001 TRP M 47 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.01212 (37438) covalent geometry : angle 2.21232 (50792) hydrogen bonds : bond 0.05331 ( 1679) hydrogen bonds : angle 4.19323 ( 5037) metal coordination : bond 0.04374 ( 36) metal coordination : angle 28.93541 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11781.93 seconds wall clock time: 201 minutes 7.24 seconds (12067.24 seconds total)