Starting phenix.real_space_refine on Mon Jul 6 14:20:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p7k_13238/07_2026/7p7k_13238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p7k_13238/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7p7k_13238/07_2026/7p7k_13238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p7k_13238/07_2026/7p7k_13238.map" model { file = "/net/cci-nas-00/data/ceres_data/7p7k_13238/07_2026/7p7k_13238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p7k_13238/07_2026/7p7k_13238.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7p7k_13238/07_2026/7p7k_13238.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p7k_13238/07_2026/7p7k_13238.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.55, per 1000 atoms: 0.21 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: 3.29 Conformation dependent library (CDL) restraints added in 1.7 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: 0.86 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: 6.53 Time building geometry restraints manager: 4.28 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=" 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 bond pdb=" O13 3PE A 201 " pdb=" P 3PE A 201 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.02e+00 bond pdb=" O13 3PE M1002 " pdb=" P 3PE M1002 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" O13 3PE M1003 " pdb=" P 3PE M1003 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 8.87e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.82e+00 ... (remaining 37433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 50018 2.33 - 4.67: 660 4.67 - 7.00: 87 7.00 - 9.34: 23 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 - 33.98: 21569 33.98 - 67.95: 341 67.95 - 101.93: 19 101.93 - 135.91: 0 135.91 - 169.88: 1 Dihedral angle restraints: 21930 sinusoidal: 8706 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 21927 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: 6349 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 6346 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: 0.420 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: 0.790 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 37.090 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 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= 0.265 Angle : 0.732 15.224 50885 Z= 0.373 Chirality : 1.482 21.178 5683 Planarity : 0.006 0.085 6349 Dihedral : 12.510 169.882 13470 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/Z covalent geometry : bond 0.00608 / 0.26 (37438) covalent geometry : angle 0.70930 / 0.37 (50792) hydrogen bonds : bond 0.06097 / 4.00 ( 1679) hydrogen bonds : angle 4.68356 / 3.32 ( 5037) metal coordination : bond 0.06212 / 4.33 ( 36) metal coordination : angle 4.26977 / 2.98 ( 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 : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 0.8567 (ttp-170) REVERT: E 112 LYS cc_start: 0.8440 (tptm) cc_final: 0.8221 (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: 0.8566 (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: 0.2541 time to fit residues: 267.8947 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 : 1.486 ------------------------------------------------------------------------------- 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... 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 = 0.3190 r_free = 0.3190 target = 0.078089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.057841 restraints weight = 59589.760| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 1.48 r_work: 0.2596 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 37474 Z= 0.417 Angle : 2.530 57.403 50885 Z= 1.454 Chirality : 0.453 6.582 5683 Planarity : 0.005 0.069 6349 Dihedral : 7.256 170.325 5390 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.20 % Favored : 97.77 % Rotamer: Outliers : 1.76 % Allowed : 8.14 % Favored : 90.10 % 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: 1.05 (0.10), residues: 2652 sheet: -0.43 (0.30), residues: 296 loop : -0.78 (0.15), residues: 1636 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/Z covalent geometry : bond 0.01171 / 0.41 (37438) covalent geometry : angle 2.20732 / 1.45 (50792) hydrogen bonds : bond 0.05326 / 3.49 ( 1679) hydrogen bonds : angle 4.28699 / 3.04 ( 5037) metal coordination : bond 0.05628 / 3.66 ( 36) metal coordination : angle 29.01886 / 20.32 ( 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 556 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 490 time to evaluate : 1.561 Fit side-chains revert: symmetry clash REVERT: F 250 MET cc_start: 0.9041 (mtt) cc_final: 0.8833 (mtt) REVERT: E 114 ASN cc_start: 0.8978 (t0) cc_final: 0.8646 (t0) REVERT: G 56 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8493 (mm-40) REVERT: G 901 HIS cc_start: 0.8221 (p90) cc_final: 0.7904 (p-80) REVERT: C 36 ASP cc_start: 0.8342 (p0) cc_final: 0.8132 (p0) REVERT: C 243 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8905 (p) REVERT: C 597 ASP cc_start: 0.8565 (t0) cc_final: 0.8240 (t0) REVERT: I 147 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: H 152 GLN cc_start: 0.8687 (tt0) cc_final: 0.8423 (tt0) REVERT: H 229 TYR cc_start: 0.8353 (m-80) cc_final: 0.7881 (m-80) REVERT: H 285 ILE cc_start: 0.9042 (mm) cc_final: 0.8814 (mm) REVERT: H 298 MET cc_start: 0.8816 (mmp) cc_final: 0.8600 (mmp) REVERT: H 322 TRP cc_start: 0.8050 (t60) cc_final: 0.7745 (t-100) REVERT: L 150 SER cc_start: 0.9343 (t) cc_final: 0.8949 (m) REVERT: L 315 GLN cc_start: 0.8959 (mm110) cc_final: 0.8730 (mm-40) REVERT: M 152 PHE cc_start: 0.8210 (m-10) cc_final: 0.7968 (m-10) REVERT: M 224 MET cc_start: 0.8874 (tmm) cc_final: 0.8100 (tmm) REVERT: M 373 MET cc_start: 0.8760 (mmm) cc_final: 0.8499 (mmm) REVERT: N 1 MET cc_start: 0.7041 (mtp) cc_final: 0.5832 (ttp) REVERT: J 94 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8584 (mm) outliers start: 66 outliers final: 41 residues processed: 540 average time/residue: 0.2536 time to fit residues: 220.6212 Evaluate side-chains 501 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 456 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 450 optimal weight: 6.9990 chunk 307 optimal weight: 5.9990 chunk 75 optimal weight: 0.0970 chunk 319 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 chunk 452 optimal weight: 0.0670 chunk 143 optimal weight: 9.9990 chunk 422 optimal weight: 5.9990 chunk 313 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 overall best weight: 3.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3193 r_free = 0.3193 target = 0.078219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.058022 restraints weight = 59286.321| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 1.47 r_work: 0.2604 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1268 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= 0.409 Angle : 2.522 57.841 50885 Z= 1.450 Chirality : 0.449 6.522 5683 Planarity : 0.004 0.067 6349 Dihedral : 7.017 170.583 5372 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.29 % Favored : 97.69 % Rotamer: Outliers : 2.18 % Allowed : 8.62 % Favored : 89.20 % 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: 0.78 (0.12), residues: 4584 helix: 1.38 (0.10), residues: 2653 sheet: -0.35 (0.30), residues: 299 loop : -0.68 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 804 TYR 0.025 0.002 TYR M 435 PHE 0.027 0.002 PHE L 341 TRP 0.024 0.001 TRP M 47 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01172 / 0.41 (37438) covalent geometry : angle 2.19873 / 1.45 (50792) hydrogen bonds : bond 0.05027 / 3.29 ( 1679) hydrogen bonds : angle 4.16554 / 2.96 ( 5037) metal coordination : bond 0.04318 / 2.73 ( 36) metal coordination : angle 28.99434 / 20.25 ( 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: 82 poor density : 470 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: F 250 MET cc_start: 0.9027 (mtt) cc_final: 0.8797 (mtt) REVERT: E 154 THR cc_start: 0.8935 (p) cc_final: 0.8732 (p) REVERT: G 215 GLU cc_start: 0.8240 (tp30) cc_final: 0.8004 (tp30) REVERT: G 617 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8297 (mp0) REVERT: G 901 HIS cc_start: 0.8231 (p90) cc_final: 0.7870 (p-80) REVERT: C 597 ASP cc_start: 0.8523 (t0) cc_final: 0.8285 (t0) REVERT: B 170 MET cc_start: 0.8583 (mmt) cc_final: 0.8368 (mmt) REVERT: I 147 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: I 153 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7014 (mmt) REVERT: H 152 GLN cc_start: 0.8622 (tt0) cc_final: 0.8377 (tt0) REVERT: H 229 TYR cc_start: 0.8379 (m-80) cc_final: 0.7807 (m-80) REVERT: H 285 ILE cc_start: 0.9004 (mm) cc_final: 0.8800 (mm) REVERT: H 298 MET cc_start: 0.8771 (mmp) cc_final: 0.8561 (mmp) REVERT: H 322 TRP cc_start: 0.8086 (t60) cc_final: 0.7828 (t-100) REVERT: M 152 PHE cc_start: 0.8123 (m-10) cc_final: 0.7911 (m-10) REVERT: M 224 MET cc_start: 0.8869 (tmm) cc_final: 0.8609 (tmm) REVERT: M 373 MET cc_start: 0.8774 (mmm) cc_final: 0.8521 (mmm) REVERT: N 1 MET cc_start: 0.7051 (mtp) cc_final: 0.5869 (ttp) REVERT: K 31 MET cc_start: 0.9024 (mtp) cc_final: 0.8802 (mtm) REVERT: J 72 MET cc_start: 0.8276 (mmt) cc_final: 0.8057 (mmt) REVERT: J 94 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8604 (mm) REVERT: J 116 ASP cc_start: 0.8604 (t70) cc_final: 0.8390 (t0) outliers start: 82 outliers final: 52 residues processed: 533 average time/residue: 0.2464 time to fit residues: 212.3377 Evaluate side-chains 508 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 452 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 46 GLN 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 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 22 ARG 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 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 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: 1.9990 chunk 193 optimal weight: 8.9990 chunk 267 optimal weight: 50.0000 chunk 363 optimal weight: 10.0000 chunk 392 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 340 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 453 optimal weight: 0.9980 chunk 319 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 53 GLN F 304 HIS F 425 GLN E 106 GLN B 47 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 261 GLN H 296 GLN H 312 ASN ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 317 GLN N 404 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.080419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.060834 restraints weight = 59377.999| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.40 r_work: 0.2670 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1525 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 55.669 50885 Z= 1.446 Chirality : 0.445 6.399 5683 Planarity : 0.004 0.066 6349 Dihedral : 6.601 170.184 5371 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.10 % Allowed : 9.04 % Favored : 88.85 % 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: 1.13 (0.12), residues: 4584 helix: 1.69 (0.10), residues: 2647 sheet: -0.28 (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/Z covalent geometry : bond 0.01137 / 0.39 (37438) covalent geometry : angle 2.18780 / 1.44 (50792) hydrogen bonds : bond 0.04175 / 2.73 ( 1679) hydrogen bonds : angle 3.92683 / 2.79 ( 5037) metal coordination : bond 0.02618 / 1.63 ( 36) metal coordination : angle 29.13558 / 20.36 ( 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 571 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 492 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 MET cc_start: 0.9061 (mmm) cc_final: 0.8838 (mmm) REVERT: F 250 MET cc_start: 0.9028 (mtt) cc_final: 0.8788 (mtt) REVERT: E 114 ASN cc_start: 0.8860 (t0) cc_final: 0.8636 (t0) REVERT: G 215 GLU cc_start: 0.8239 (tp30) cc_final: 0.7997 (tp30) REVERT: G 617 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: G 901 HIS cc_start: 0.8142 (p90) cc_final: 0.7822 (p-80) REVERT: C 597 ASP cc_start: 0.8467 (t0) cc_final: 0.8234 (t0) REVERT: I 153 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.6934 (mmt) REVERT: H 296 GLN cc_start: 0.8596 (mt0) cc_final: 0.8289 (mt0) REVERT: H 322 TRP cc_start: 0.8043 (t60) cc_final: 0.7736 (t-100) REVERT: L 407 MET cc_start: 0.8572 (tpp) cc_final: 0.8021 (tpp) REVERT: M 224 MET cc_start: 0.8794 (tmm) cc_final: 0.8096 (tmm) REVERT: M 373 MET cc_start: 0.8724 (mmm) cc_final: 0.8516 (mmm) REVERT: M 429 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7910 (tt) REVERT: N 1 MET cc_start: 0.7074 (mtp) cc_final: 0.5874 (ttp) REVERT: N 63 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8301 (p) REVERT: J 6 TYR cc_start: 0.8887 (m-80) cc_final: 0.8603 (m-80) REVERT: J 116 ASP cc_start: 0.8361 (t70) cc_final: 0.8132 (t0) REVERT: J 117 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8325 (mm-40) outliers start: 79 outliers final: 43 residues processed: 550 average time/residue: 0.2487 time to fit residues: 219.6685 Evaluate side-chains 508 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 461 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 326 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 750 ARG 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 B residue 71 SER 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 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 372 ILE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 491 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 63 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 103 ASP 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 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 2 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 chunk 115 optimal weight: 0.1980 chunk 360 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 214 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 443 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 22 GLN F 237 GLN F 304 HIS F 425 GLN E 106 GLN G 224 GLN G 352 GLN G 808 GLN B 47 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 GLN ** 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 J 115 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.077993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.057868 restraints weight = 59088.861| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 1.48 r_work: 0.2599 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 37474 Z= 0.416 Angle : 2.523 54.933 50885 Z= 1.451 Chirality : 0.450 6.507 5683 Planarity : 0.004 0.067 6349 Dihedral : 6.753 170.260 5358 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.38 % Favored : 97.60 % Rotamer: Outliers : 1.94 % Allowed : 9.66 % 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: 1.13 (0.12), residues: 4584 helix: 1.66 (0.10), residues: 2653 sheet: -0.33 (0.30), residues: 308 loop : -0.52 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 664 TYR 0.021 0.002 TYR L 428 PHE 0.025 0.002 PHE L 341 TRP 0.024 0.001 TRP M 47 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01185 / 0.41 (37438) covalent geometry : angle 2.20119 / 1.45 (50792) hydrogen bonds : bond 0.05023 / 3.29 ( 1679) hydrogen bonds : angle 4.08136 / 2.90 ( 5037) metal coordination : bond 0.04149 / 2.68 ( 36) metal coordination : angle 28.93313 / 20.25 ( 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 537 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 464 time to evaluate : 1.242 Fit side-chains REVERT: F 250 MET cc_start: 0.9048 (mtt) cc_final: 0.8807 (mtt) REVERT: E 114 ASN cc_start: 0.8960 (t0) cc_final: 0.8692 (t0) REVERT: G 617 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: G 901 HIS cc_start: 0.8257 (p90) cc_final: 0.7904 (p-80) REVERT: C 469 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9112 (mp) REVERT: I 153 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7082 (mmt) REVERT: H 273 LEU cc_start: 0.9010 (tp) cc_final: 0.8799 (mt) REVERT: H 322 TRP cc_start: 0.8124 (t60) cc_final: 0.7811 (t-100) REVERT: L 407 MET cc_start: 0.8446 (tpp) cc_final: 0.8051 (tpp) REVERT: M 224 MET cc_start: 0.8822 (tmm) cc_final: 0.8106 (tmm) REVERT: M 429 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8035 (tt) REVERT: M 447 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8457 (mmtm) REVERT: N 1 MET cc_start: 0.7111 (mtp) cc_final: 0.6014 (ttp) REVERT: N 57 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8381 (mm110) REVERT: N 63 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8474 (p) REVERT: J 72 MET cc_start: 0.8361 (mmt) cc_final: 0.8103 (mmt) REVERT: J 116 ASP cc_start: 0.8430 (t70) cc_final: 0.8166 (t0) outliers start: 73 outliers final: 53 residues processed: 519 average time/residue: 0.2346 time to fit residues: 197.1645 Evaluate side-chains 512 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 454 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 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 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 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 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 152 GLN Chi-restraints excluded: chain H residue 165 MET 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 391 LEU 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 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 46 PHE Chi-restraints excluded: chain K residue 92 ILE 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: 9.9990 chunk 138 optimal weight: 0.0000 chunk 232 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 282 optimal weight: 3.9990 chunk 333 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 chunk 189 optimal weight: 0.7980 chunk 375 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 237 GLN F 304 HIS F 425 GLN E 106 GLN B 47 ASN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 232 GLN N 317 GLN N 404 GLN K 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.080037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.060577 restraints weight = 59354.424| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.38 r_work: 0.2663 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1664 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= 0.388 Angle : 2.516 55.104 50885 Z= 1.447 Chirality : 0.446 6.418 5683 Planarity : 0.004 0.065 6349 Dihedral : 6.489 170.296 5356 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.84 % Allowed : 9.98 % Favored : 88.19 % 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: 1.28 (0.12), residues: 4584 helix: 1.79 (0.10), residues: 2649 sheet: -0.32 (0.30), residues: 309 loop : -0.44 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 804 TYR 0.025 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/Z covalent geometry : bond 0.01140 / 0.39 (37438) covalent geometry : angle 2.18897 / 1.44 (50792) hydrogen bonds : bond 0.04300 / 2.81 ( 1679) hydrogen bonds : angle 3.91386 / 2.78 ( 5037) metal coordination : bond 0.02852 / 1.85 ( 36) metal coordination : angle 29.07849 / 20.36 ( 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: 69 poor density : 467 time to evaluate : 1.434 Fit side-chains REVERT: F 250 MET cc_start: 0.9028 (mtt) cc_final: 0.8775 (mtt) REVERT: E 114 ASN cc_start: 0.8864 (t0) cc_final: 0.8620 (t0) REVERT: G 617 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: G 901 HIS cc_start: 0.8140 (p90) cc_final: 0.7791 (p-80) REVERT: C 469 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9109 (mp) REVERT: C 597 ASP cc_start: 0.8380 (t0) cc_final: 0.7938 (t70) REVERT: B 174 GLU cc_start: 0.8271 (tt0) cc_final: 0.7990 (pt0) REVERT: I 153 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.6994 (mmt) REVERT: H 32 MET cc_start: 0.4507 (mtt) cc_final: 0.3936 (mtt) REVERT: H 268 PHE cc_start: 0.7806 (t80) cc_final: 0.7603 (t80) REVERT: H 322 TRP cc_start: 0.8086 (t60) cc_final: 0.7778 (t-100) REVERT: M 146 MET cc_start: 0.8230 (ptt) cc_final: 0.7534 (ptt) REVERT: M 224 MET cc_start: 0.8801 (tmm) cc_final: 0.8104 (tmm) REVERT: M 429 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7859 (tt) REVERT: N 1 MET cc_start: 0.7103 (mtp) cc_final: 0.5918 (ttp) REVERT: N 63 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8262 (p) REVERT: J 6 TYR cc_start: 0.8922 (m-80) cc_final: 0.8629 (m-80) outliers start: 69 outliers final: 52 residues processed: 521 average time/residue: 0.2298 time to fit residues: 194.3738 Evaluate side-chains 510 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 453 time to evaluate : 1.683 ------------------------------------------------------------------------------- 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 E residue 46 GLN 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 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 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 127 PHE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 474 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 12 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 116 ILE 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 318 TYR Chi-restraints excluded: chain L residue 352 VAL Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 391 LEU 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 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 46 PHE 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: 4.9990 chunk 63 optimal weight: 3.9990 chunk 290 optimal weight: 9.9990 chunk 453 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 446 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 238 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 237 GLN F 304 HIS F 425 GLN E 106 GLN B 47 ASN B 92 GLN H 296 GLN L 62 GLN M 159 HIS ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.078280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.058134 restraints weight = 59334.076| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.45 r_work: 0.2607 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 37474 Z= 0.409 Angle : 2.522 54.303 50885 Z= 1.450 Chirality : 0.449 6.498 5683 Planarity : 0.004 0.066 6349 Dihedral : 6.702 170.273 5356 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.36 % Favored : 97.62 % Rotamer: Outliers : 2.00 % Allowed : 10.08 % Favored : 87.92 % 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: 1.23 (0.12), residues: 4584 helix: 1.73 (0.10), residues: 2657 sheet: -0.33 (0.30), residues: 307 loop : -0.44 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 664 TYR 0.021 0.002 TYR L 428 PHE 0.025 0.002 PHE L 341 TRP 0.025 0.001 TRP M 47 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01172 / 0.41 (37438) covalent geometry : angle 2.19940 / 1.45 (50792) hydrogen bonds : bond 0.04880 / 3.20 ( 1679) hydrogen bonds : angle 4.03571 / 2.87 ( 5037) metal coordination : bond 0.03913 / 2.54 ( 36) metal coordination : angle 28.95418 / 20.27 ( 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 527 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 452 time to evaluate : 1.338 Fit side-chains REVERT: F 250 MET cc_start: 0.9050 (mtt) cc_final: 0.8792 (mtt) REVERT: E 114 ASN cc_start: 0.8906 (t0) cc_final: 0.8657 (t0) REVERT: G 562 ARG cc_start: 0.8989 (mtm-85) cc_final: 0.8582 (mtm-85) REVERT: G 617 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: G 901 HIS cc_start: 0.8220 (p90) cc_final: 0.7864 (p-80) REVERT: C 469 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9114 (mp) REVERT: C 597 ASP cc_start: 0.8487 (t0) cc_final: 0.8164 (t70) REVERT: I 153 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7097 (mmt) REVERT: H 32 MET cc_start: 0.4447 (OUTLIER) cc_final: 0.3439 (mtt) REVERT: H 147 MET cc_start: 0.7850 (mmt) cc_final: 0.7608 (mmt) REVERT: H 322 TRP cc_start: 0.8139 (t60) cc_final: 0.7801 (t-100) REVERT: M 224 MET cc_start: 0.8820 (tmm) cc_final: 0.8126 (tmm) REVERT: M 429 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7958 (tt) REVERT: N 1 MET cc_start: 0.7117 (mtp) cc_final: 0.5871 (ttp) REVERT: N 63 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8306 (p) REVERT: N 232 GLN cc_start: 0.8902 (tt0) cc_final: 0.8676 (tt0) REVERT: J 64 MET cc_start: 0.8864 (mmp) cc_final: 0.8488 (mmp) outliers start: 75 outliers final: 57 residues processed: 509 average time/residue: 0.2252 time to fit residues: 185.8507 Evaluate side-chains 511 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 448 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 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 92 GLN 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 32 MET 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 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 391 LEU 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 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: 6.9990 chunk 274 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 367 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 256 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 237 GLN F 304 HIS F 425 GLN E 106 GLN G 828 GLN B 43 ASN B 47 ASN H 152 GLN H 192 GLN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.078065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.057874 restraints weight = 59233.149| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 1.47 r_work: 0.2601 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 37474 Z= 0.412 Angle : 2.524 54.117 50885 Z= 1.451 Chirality : 0.449 6.493 5683 Planarity : 0.004 0.070 6349 Dihedral : 6.810 170.443 5356 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.38 % Favored : 97.60 % Rotamer: Outliers : 2.10 % Allowed : 10.03 % Favored : 87.87 % 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: 1.21 (0.12), residues: 4584 helix: 1.71 (0.10), residues: 2654 sheet: -0.51 (0.29), residues: 317 loop : -0.39 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 804 TYR 0.021 0.002 TYR L 428 PHE 0.025 0.002 PHE L 341 TRP 0.026 0.001 TRP M 47 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01177 / 0.41 (37438) covalent geometry : angle 2.20151 / 1.45 (50792) hydrogen bonds : bond 0.04971 / 3.26 ( 1679) hydrogen bonds : angle 4.07240 / 2.89 ( 5037) metal coordination : bond 0.03927 / 2.56 ( 36) metal coordination : angle 28.95895 / 20.26 ( 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 534 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 455 time to evaluate : 1.447 Fit side-chains REVERT: F 182 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: F 250 MET cc_start: 0.9054 (mtt) cc_final: 0.8805 (mtt) REVERT: E 114 ASN cc_start: 0.8935 (t0) cc_final: 0.8695 (t0) REVERT: G 562 ARG cc_start: 0.8993 (mtm-85) cc_final: 0.8583 (mtm-85) REVERT: G 617 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: C 469 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9115 (mp) REVERT: C 597 ASP cc_start: 0.8455 (t0) cc_final: 0.8184 (t0) REVERT: I 153 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7027 (mtt) REVERT: H 32 MET cc_start: 0.4561 (OUTLIER) cc_final: 0.3589 (mtt) REVERT: H 147 MET cc_start: 0.7835 (mmt) cc_final: 0.7616 (mmt) REVERT: H 209 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7725 (mmm160) REVERT: H 322 TRP cc_start: 0.8141 (t60) cc_final: 0.7816 (t-100) REVERT: M 224 MET cc_start: 0.8834 (tmm) cc_final: 0.8115 (tmm) REVERT: M 429 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7947 (tt) REVERT: N 1 MET cc_start: 0.7097 (mtp) cc_final: 0.6044 (ttp) REVERT: N 63 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8282 (p) REVERT: N 324 GLU cc_start: 0.8448 (tt0) cc_final: 0.8188 (tt0) REVERT: J 94 ILE cc_start: 0.9067 (tp) cc_final: 0.8695 (mt) outliers start: 79 outliers final: 62 residues processed: 514 average time/residue: 0.2449 time to fit residues: 203.9532 Evaluate side-chains 519 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 450 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 182 GLU 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 261 HIS 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 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 32 MET 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 245 ILE 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 391 LEU Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 491 LEU 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 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: 10.0000 chunk 280 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 336 optimal weight: 9.9990 chunk 378 optimal weight: 8.9990 chunk 448 optimal weight: 0.3980 chunk 48 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 243 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 237 GLN F 304 HIS F 425 GLN E 106 GLN G 490 GLN G 583 ASN G 901 HIS B 47 ASN B 92 GLN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 232 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.058370 restraints weight = 59094.392| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 1.46 r_work: 0.2612 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1691 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 : 2.523 54.477 50885 Z= 1.450 Chirality : 0.448 6.470 5683 Planarity : 0.004 0.066 6349 Dihedral : 6.788 170.448 5356 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.08 % Allowed : 10.11 % 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: 1.25 (0.12), residues: 4584 helix: 1.74 (0.10), residues: 2654 sheet: -0.49 (0.29), residues: 315 loop : -0.37 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 804 TYR 0.021 0.001 TYR L 428 PHE 0.026 0.001 PHE L 341 TRP 0.026 0.001 TRP M 47 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01158 / 0.40 (37438) covalent geometry : angle 2.19906 / 1.45 (50792) hydrogen bonds : bond 0.04794 / 3.14 ( 1679) hydrogen bonds : angle 4.04217 / 2.87 ( 5037) metal coordination : bond 0.03594 / 2.35 ( 36) metal coordination : angle 28.99859 / 20.32 ( 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 535 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 457 time to evaluate : 1.465 Fit side-chains REVERT: F 182 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: F 250 MET cc_start: 0.9056 (mtt) cc_final: 0.8799 (mtt) REVERT: E 114 ASN cc_start: 0.8917 (t0) cc_final: 0.8662 (t0) REVERT: G 562 ARG cc_start: 0.8985 (mtm-85) cc_final: 0.8563 (mtm-85) REVERT: G 617 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: C 394 TYR cc_start: 0.7854 (m-80) cc_final: 0.7567 (m-80) REVERT: C 469 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9114 (mp) REVERT: C 597 ASP cc_start: 0.8464 (t0) cc_final: 0.8202 (t0) REVERT: I 153 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7081 (mmt) REVERT: H 32 MET cc_start: 0.5023 (OUTLIER) cc_final: 0.4114 (mtt) REVERT: H 59 GLN cc_start: 0.8768 (tm-30) cc_final: 0.7558 (mm-40) REVERT: H 209 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7318 (mmm160) REVERT: H 268 PHE cc_start: 0.7891 (t80) cc_final: 0.7599 (t80) REVERT: H 322 TRP cc_start: 0.8146 (t60) cc_final: 0.7815 (t-100) REVERT: M 224 MET cc_start: 0.8823 (tmm) cc_final: 0.8107 (tmm) REVERT: M 429 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7921 (tt) REVERT: N 1 MET cc_start: 0.7047 (mtp) cc_final: 0.5817 (ttp) REVERT: N 63 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8161 (p) REVERT: N 324 GLU cc_start: 0.8447 (tt0) cc_final: 0.8202 (tt0) REVERT: K 88 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8256 (mp10) REVERT: J 64 MET cc_start: 0.8879 (mmp) cc_final: 0.8422 (mmp) REVERT: J 72 MET cc_start: 0.8292 (mmt) cc_final: 0.7821 (mmt) REVERT: J 94 ILE cc_start: 0.9064 (tp) cc_final: 0.8691 (mt) outliers start: 78 outliers final: 66 residues processed: 514 average time/residue: 0.2439 time to fit residues: 202.9253 Evaluate side-chains 523 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 450 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 182 GLU 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 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 474 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 92 GLN 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 12 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 32 MET 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 245 ILE 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 391 LEU Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 491 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 102 optimal weight: 0.1980 chunk 121 optimal weight: 0.2980 chunk 286 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 406 optimal weight: 3.9990 chunk 337 optimal weight: 0.9980 chunk 392 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 413 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 237 GLN F 304 HIS F 425 GLN E 106 GLN G 583 ASN G 901 HIS ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 HIS N 149 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.059636 restraints weight = 59425.090| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.48 r_work: 0.2645 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1794 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= 0.389 Angle : 2.523 54.461 50885 Z= 1.449 Chirality : 0.446 6.412 5683 Planarity : 0.004 0.065 6349 Dihedral : 6.638 170.334 5356 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.76 % Allowed : 10.43 % 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: 1.34 (0.12), residues: 4584 helix: 1.82 (0.10), residues: 2649 sheet: -0.47 (0.29), residues: 317 loop : -0.33 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 804 TYR 0.025 0.001 TYR N 424 PHE 0.026 0.001 PHE L 341 TRP 0.033 0.001 TRP H 135 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01139 / 0.39 (37438) covalent geometry : angle 2.19728 / 1.45 (50792) hydrogen bonds : bond 0.04429 / 2.90 ( 1679) hydrogen bonds : angle 3.96152 / 2.81 ( 5037) metal coordination : bond 0.02856 / 1.85 ( 36) metal coordination : angle 29.08325 / 20.38 ( 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 530 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 464 time to evaluate : 1.327 Fit side-chains REVERT: F 182 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: F 250 MET cc_start: 0.9061 (mtt) cc_final: 0.8806 (mtt) REVERT: E 114 ASN cc_start: 0.8900 (t0) cc_final: 0.8652 (t0) REVERT: G 562 ARG cc_start: 0.8975 (mtm-85) cc_final: 0.8556 (mtm-85) REVERT: G 617 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: C 469 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9108 (mp) REVERT: C 597 ASP cc_start: 0.8474 (t0) cc_final: 0.8189 (t0) REVERT: I 153 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.6996 (mmt) REVERT: H 209 ARG cc_start: 0.7839 (mmm160) cc_final: 0.7275 (mmm160) REVERT: H 213 ASP cc_start: 0.5826 (t0) cc_final: 0.5570 (t0) REVERT: H 268 PHE cc_start: 0.7904 (t80) cc_final: 0.7497 (t80) REVERT: H 322 TRP cc_start: 0.8128 (t60) cc_final: 0.7811 (t-100) REVERT: M 224 MET cc_start: 0.8783 (tmm) cc_final: 0.8064 (tmm) REVERT: M 253 THR cc_start: 0.8022 (p) cc_final: 0.7574 (m) REVERT: M 429 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7839 (tt) REVERT: N 1 MET cc_start: 0.7034 (mtp) cc_final: 0.5793 (ttp) REVERT: N 63 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.7937 (p) REVERT: N 321 MET cc_start: 0.7542 (ptp) cc_final: 0.7270 (ptp) REVERT: N 324 GLU cc_start: 0.8443 (tt0) cc_final: 0.8210 (tt0) REVERT: K 88 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8277 (mp10) REVERT: J 6 TYR cc_start: 0.8964 (m-80) cc_final: 0.8705 (m-80) REVERT: J 64 MET cc_start: 0.8857 (mmp) cc_final: 0.8508 (mmp) REVERT: J 72 MET cc_start: 0.8192 (mmt) cc_final: 0.7959 (mmp) REVERT: J 94 ILE cc_start: 0.9054 (tp) cc_final: 0.8695 (mt) outliers start: 66 outliers final: 51 residues processed: 514 average time/residue: 0.2174 time to fit residues: 180.1885 Evaluate side-chains 515 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 458 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 182 GLU 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 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 750 ARG Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 GLU 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 81 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 245 ILE 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 391 LEU Chi-restraints excluded: chain L residue 400 ASP Chi-restraints excluded: chain L residue 491 LEU 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 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 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 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 365 optimal weight: 0.8980 chunk 272 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 327 optimal weight: 3.9990 chunk 358 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 152 GLN H 192 GLN ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN L 62 GLN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN N 232 GLN ** N 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.079740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.059938 restraints weight = 58949.963| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 1.41 r_work: 0.2652 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 37474 Z= 0.390 Angle : 2.521 53.801 50885 Z= 1.449 Chirality : 0.446 6.417 5683 Planarity : 0.004 0.064 6349 Dihedral : 6.559 170.120 5355 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.70 % Allowed : 10.64 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.13 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: 1.38 (0.13), residues: 4584 helix: 1.84 (0.10), residues: 2651 sheet: -0.43 (0.30), residues: 316 loop : -0.30 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 804 TYR 0.024 0.001 TYR N 424 PHE 0.026 0.001 PHE L 341 TRP 0.027 0.001 TRP M 47 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01142 / 0.39 (37438) covalent geometry : angle 2.19559 / 1.45 (50792) hydrogen bonds : bond 0.04381 / 2.87 ( 1679) hydrogen bonds : angle 3.93708 / 2.79 ( 5037) metal coordination : bond 0.02893 / 1.85 ( 36) metal coordination : angle 29.05700 / 20.35 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12022.74 seconds wall clock time: 205 minutes 53.42 seconds (12353.42 seconds total)