Starting phenix.real_space_refine on Thu Mar 5 18:26:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nmi_0452/03_2026/6nmi_0452.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nmi_0452/03_2026/6nmi_0452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nmi_0452/03_2026/6nmi_0452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nmi_0452/03_2026/6nmi_0452.map" model { file = "/net/cci-nas-00/data/ceres_data/6nmi_0452/03_2026/6nmi_0452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nmi_0452/03_2026/6nmi_0452.cif" } resolution = 3.7 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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 S 141 5.16 5 C 15472 2.51 5 N 4259 2.21 5 O 4497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24379 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1355 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 10, 'TRANS': 159} Chain: "A" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3835 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 4, 'PTRANS': 15, 'TRANS': 463} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2361 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 277} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3679 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 451} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 207 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 546 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'UNK:plan-1': 33} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 846 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'UNK:plan-1': 71} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 375 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 276 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 407 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 67} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'UNK:plan-1': 49} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3589 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 429} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1810 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 10, 'TRANS': 233} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'UNK:plan-1': 35} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 900 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2065 Classifications: {'peptide': 263} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 253} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "H" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1592 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 202} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 81 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: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6122 SG CYS B 116 31.188 92.936 92.618 1.00 57.98 S ATOM 6431 SG CYS B 155 25.509 94.811 95.777 1.00 71.14 S ATOM 6262 SG CYS B 134 29.804 98.669 94.897 1.00 58.64 S ATOM 6720 SG CYS B 190 29.808 93.756 99.287 1.00 60.71 S ATOM 19864 SG CYS E 345 106.926 53.182 92.189 1.00 75.65 S ATOM 19886 SG CYS E 348 108.467 51.856 88.413 1.00 64.83 S ATOM 20043 SG CYS E 368 106.401 56.196 89.757 1.00 71.71 S ATOM 20064 SG CYS E 371 104.697 52.665 89.750 1.00 71.32 S ATOM 19984 SG CYS E 360 96.585 51.420 99.170 1.00 84.88 S ATOM 20002 SG CYS E 363 99.750 48.979 100.284 1.00 87.91 S ATOM 20151 SG CYS E 382 98.330 48.895 96.556 1.00 71.58 S ATOM 20168 SG CYS E 385 95.940 47.256 99.392 1.00 74.09 S ATOM 19428 SG CYS E 291 71.907 29.161 73.434 1.00 79.05 S ATOM 19450 SG CYS E 294 69.682 28.269 70.220 1.00 89.45 S ATOM 19539 SG CYS E 305 69.598 31.885 71.534 1.00 81.96 S ATOM 19562 SG CYS E 308 66.943 29.397 72.226 1.00 86.60 S ATOM 22072 SG CYS F 268 71.653 40.558 91.347 1.00 65.95 S ATOM 22091 SG CYS F 271 74.687 39.238 92.484 1.00 64.03 S ATOM 22176 SG CYS F 282 71.860 38.166 94.531 1.00 77.32 S ATOM 22196 SG CYS F 285 73.237 41.680 95.218 1.00 82.61 S ATOM 22803 SG CYS H 6 23.507 133.253 59.350 1.00200.73 S ATOM 22821 SG CYS H 9 23.606 136.318 57.013 1.00206.24 S ATOM 22939 SG CYS H 31 26.156 135.891 60.585 1.00212.05 S ATOM 22955 SG CYS H 34 22.538 136.118 60.764 1.00219.26 S ATOM 22909 SG CYS H 26 15.011 138.561 70.710 1.00197.12 S ATOM 23016 SG CYS H 46 14.560 138.076 67.402 1.00221.32 S ATOM 23034 SG CYS H 49 12.266 136.988 69.848 1.00223.19 S Time building chain proxies: 4.71, per 1000 atoms: 0.19 Number of scatterers: 24379 At special positions: 0 Unit cell: (165.6, 165.6, 131.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 141 16.00 O 4497 8.00 N 4259 7.00 C 15472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 255 " - pdb=" SG CYS F 257 " distance=2.04 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 Links applied TRANS " UNK B 292 " - " GLY B 291 " " UNK C 148 " - " LEU C 147 " " UNK C 233 " - " ARG C 232 " " UNK C 390 " - " ILE C 389 " " UNK C 443 " - " GLN C 442 " " UNK C 480 " - " PHE C 479 " " UNK E 260 " - " ILE E 259 " Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 368 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb=" ZN H 400 " pdb="ZN ZN H 400 " - pdb=" SG CYS H 34 " pdb="ZN ZN H 400 " - pdb=" SG CYS H 6 " pdb="ZN ZN H 400 " - pdb=" SG CYS H 31 " pdb="ZN ZN H 400 " - pdb=" SG CYS H 9 " pdb=" ZN H 401 " pdb="ZN ZN H 401 " - pdb=" ND1 HIS H 28 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 46 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 26 " pdb="ZN ZN H 401 " - pdb=" SG CYS H 49 " Number of angles added : 33 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 21 sheets defined 54.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 92 through 104 Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.655A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 149 through 161 removed outlier: 3.677A pdb=" N MET A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 removed outlier: 4.602A pdb=" N ILE A 185 " --> pdb=" O HIS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 345 through 358 removed outlier: 4.132A pdb=" N VAL A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 420 through 431 Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 447 through 459 removed outlier: 4.129A pdb=" N GLN A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.636A pdb=" N ILE A 484 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.525A pdb=" N GLU A 495 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 525 Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.790A pdb=" N LEU A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 553 Processing helix chain 'A' and resid 564 through 576 removed outlier: 3.743A pdb=" N LEU A 568 " --> pdb=" O ASN A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 598 removed outlier: 4.037A pdb=" N HIS A 598 " --> pdb=" O GLN A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 612 Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.660A pdb=" N GLU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 684 removed outlier: 4.408A pdb=" N TYR A 672 " --> pdb=" O GLN A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 718 removed outlier: 3.513A pdb=" N GLN A 710 " --> pdb=" O LYS A 706 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 34 removed outlier: 3.740A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 76 through 98 removed outlier: 3.653A pdb=" N GLU B 98 " --> pdb=" O TYR B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.532A pdb=" N GLN B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 238 through 248 Processing helix chain 'B' and resid 253 through 277 Processing helix chain 'B' and resid 278 through 290 Processing helix chain 'B' and resid 325 through 345 Processing helix chain 'B' and resid 353 through 365 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 390 through 393 Processing helix chain 'B' and resid 394 through 408 removed outlier: 3.804A pdb=" N THR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 removed outlier: 4.068A pdb=" N ILE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Proline residue: B 446 - end of helix Processing helix chain 'B' and resid 467 through 472 removed outlier: 3.898A pdb=" N ASP B 472 " --> pdb=" O PRO B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 531 Processing helix chain 'B' and resid 541 through 551 Processing helix chain 'B' and resid 557 through 565 Processing helix chain 'B' and resid 575 through 588 Processing helix chain 'B' and resid 602 through 606 removed outlier: 3.689A pdb=" N SER B 605 " --> pdb=" O GLY B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 643 removed outlier: 4.132A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 665 removed outlier: 3.645A pdb=" N THR B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 686 removed outlier: 3.571A pdb=" N PHE B 684 " --> pdb=" O ASP B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 693 removed outlier: 3.527A pdb=" N LYS B 692 " --> pdb=" O LYS B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 709 through 724 Processing helix chain 'B' and resid 729 through 733 Processing helix chain 'B' and resid 746 through 756 Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.522A pdb=" N GLU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 132 Processing helix chain 'C' and resid 138 through 145 Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 240 through 256 Processing helix chain 'C' and resid 295 through 318 Processing helix chain 'C' and resid 347 through 359 removed outlier: 3.792A pdb=" N GLU C 359 " --> pdb=" O GLN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 384 Processing helix chain 'C' and resid 397 through 411 removed outlier: 3.589A pdb=" N ILE C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 454 through 480 Processing helix chain 'C' and resid 485 through 515 removed outlier: 3.516A pdb=" N UNK C 489 " --> pdb=" O UNK C 485 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N UNK C 515 " --> pdb=" O UNK C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 removed outlier: 3.753A pdb=" N GLU C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 37 through 46 Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.797A pdb=" N VAL D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 80 removed outlier: 3.813A pdb=" N SER D 80 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 144 through 165 Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'D' and resid 207 through 221 Processing helix chain 'D' and resid 229 through 241 removed outlier: 3.536A pdb=" N ILE D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.669A pdb=" N ASN D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 332 Processing helix chain 'D' and resid 347 through 357 Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 384 through 399 Processing helix chain 'D' and resid 415 through 428 Processing helix chain 'D' and resid 447 through 456 removed outlier: 4.316A pdb=" N VAL D 451 " --> pdb=" O GLY D 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.625A pdb=" N UNK E 20 " --> pdb=" O UNK E 17 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N UNK E 22 " --> pdb=" O UNK E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 42 Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 79 through 99 Processing helix chain 'E' and resid 123 through 135 removed outlier: 4.141A pdb=" N HIS E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 156 removed outlier: 3.512A pdb=" N SER E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 224 through 235 removed outlier: 3.593A pdb=" N TYR E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 322 removed outlier: 3.585A pdb=" N SER E 321 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR E 322 " --> pdb=" O ALA E 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 318 through 322' Processing helix chain 'E' and resid 368 through 378 Processing helix chain 'E' and resid 382 through 387 removed outlier: 3.730A pdb=" N ILE E 386 " --> pdb=" O CYS E 382 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS E 387 " --> pdb=" O PRO E 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 382 through 387' Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 33 through 52 removed outlier: 4.092A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 120 removed outlier: 3.608A pdb=" N THR F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 150 Processing helix chain 'F' and resid 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 173 through 187 removed outlier: 4.240A pdb=" N ASN F 179 " --> pdb=" O MET F 175 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL F 180 " --> pdb=" O ASN F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 210 Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 222 through 231 removed outlier: 3.893A pdb=" N TRP F 229 " --> pdb=" O GLN F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 239 removed outlier: 4.175A pdb=" N SER F 239 " --> pdb=" O GLN F 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 27 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 49 through 65 removed outlier: 4.603A pdb=" N GLY G 58 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA G 65 " --> pdb=" O MET G 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 16 Processing helix chain 'H' and resid 31 through 40 Processing helix chain 'H' and resid 65 through 80 Processing helix chain 'H' and resid 91 through 112 removed outlier: 3.732A pdb=" N TYR H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 130 removed outlier: 4.198A pdb=" N ASN H 117 " --> pdb=" O VAL H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 189 removed outlier: 3.627A pdb=" N LYS H 135 " --> pdb=" O ASP H 131 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER H 189 " --> pdb=" O ASP H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 210 removed outlier: 3.588A pdb=" N LEU H 197 " --> pdb=" O PRO H 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.365A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.618A pdb=" N GLU A 115 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 272 removed outlier: 4.497A pdb=" N TYR A 175 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 166 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLU A 294 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 168 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 406 through 409 removed outlier: 3.541A pdb=" N GLY A 365 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N MET A 438 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 466 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU A 440 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY A 336 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N THR A 467 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 338 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL A 337 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 489 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 579 through 580 removed outlier: 6.542A pdb=" N ILE A 558 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE A 607 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A 623 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU A 662 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN A 625 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER A 664 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE A 690 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU A 509 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 40 Processing sheet with id=AA8, first strand: chain 'B' and resid 106 through 108 removed outlier: 7.310A pdb=" N LEU B 107 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 252 Processing sheet with id=AB1, first strand: chain 'B' and resid 479 through 481 Processing sheet with id=AB2, first strand: chain 'B' and resid 490 through 494 removed outlier: 6.304A pdb=" N CYS B 491 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N PHE B 679 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N MET B 493 " --> pdb=" O PHE B 679 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 618 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ALA B 680 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET B 620 " --> pdb=" O ALA B 680 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 536 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE B 621 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N PHE B 538 " --> pdb=" O PHE B 621 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 100 Processing sheet with id=AB4, first strand: chain 'D' and resid 271 through 273 Processing sheet with id=AB5, first strand: chain 'D' and resid 402 through 405 Processing sheet with id=AB6, first strand: chain 'D' and resid 407 through 410 Processing sheet with id=AB7, first strand: chain 'E' and resid 113 through 121 removed outlier: 4.736A pdb=" N ALA E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS E 110 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LYS E 116 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL E 108 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU E 120 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE E 104 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL E 167 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE E 199 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE E 169 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 311 through 312 removed outlier: 4.122A pdb=" N THR E 311 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 257 through 258 Processing sheet with id=AC1, first strand: chain 'E' and resid 332 through 334 Processing sheet with id=AC2, first strand: chain 'F' and resid 67 through 71 removed outlier: 3.771A pdb=" N ARG F 68 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL F 59 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU F 11 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE F 60 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE F 13 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N SER F 62 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL F 15 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU F 10 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU F 162 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL F 12 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE F 164 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL F 14 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER F 159 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ASP F 192 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE F 161 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N CYS F 194 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL F 163 " --> pdb=" O CYS F 194 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 21 through 23 1167 hydrogen bonds defined for protein. 3384 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: 4.40 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 10371 1.43 - 1.64: 14250 1.64 - 1.86: 204 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 24837 Sorted by residual: bond pdb=" C VAL C 211 " pdb=" N PRO C 212 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.34e-02 1.83e+03 1.18e+01 bond pdb=" CA PRO H 17 " pdb=" CB PRO H 17 " ideal model delta sigma weight residual 1.531 1.552 -0.020 6.20e-03 2.60e+04 1.07e+01 bond pdb=" C CYS E 177 " pdb=" N ASP E 178 " ideal model delta sigma weight residual 1.331 1.247 0.084 2.83e-02 1.25e+03 8.75e+00 bond pdb=" C MET C 117 " pdb=" N LEU C 118 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.40e-02 5.10e+03 4.90e+00 bond pdb=" C SER B 395 " pdb=" N PRO B 396 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.58e+00 ... (remaining 24832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 32592 2.78 - 5.56: 928 5.56 - 8.34: 123 8.34 - 11.12: 25 11.12 - 13.90: 4 Bond angle restraints: 33672 Sorted by residual: angle pdb=" N VAL A 92 " pdb=" CA VAL A 92 " pdb=" C VAL A 92 " ideal model delta sigma weight residual 111.77 105.15 6.62 1.04e+00 9.25e-01 4.05e+01 angle pdb=" C TYR C 414 " pdb=" N THR C 415 " pdb=" CA THR C 415 " ideal model delta sigma weight residual 121.80 135.70 -13.90 2.44e+00 1.68e-01 3.25e+01 angle pdb=" CA GLN C 442 " pdb=" C GLN C 442 " pdb=" O GLN C 442 " ideal model delta sigma weight residual 120.80 111.48 9.32 1.70e+00 3.46e-01 3.00e+01 angle pdb=" C SER C 227 " pdb=" N HIS C 228 " pdb=" CA HIS C 228 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C UNK C 154 " pdb=" N UNK C 155 " pdb=" CA UNK C 155 " ideal model delta sigma weight residual 121.70 130.72 -9.02 1.80e+00 3.09e-01 2.51e+01 ... (remaining 33667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 14477 17.07 - 34.14: 516 34.14 - 51.21: 83 51.21 - 68.28: 12 68.28 - 85.35: 10 Dihedral angle restraints: 15098 sinusoidal: 5756 harmonic: 9342 Sorted by residual: dihedral pdb=" CA PRO C 212 " pdb=" C PRO C 212 " pdb=" N HIS C 213 " pdb=" CA HIS C 213 " ideal model delta harmonic sigma weight residual -180.00 -99.53 -80.47 0 5.00e+00 4.00e-02 2.59e+02 dihedral pdb=" CA LEU B 102 " pdb=" C LEU B 102 " pdb=" N PRO B 103 " pdb=" CA PRO B 103 " ideal model delta harmonic sigma weight residual -180.00 -123.78 -56.22 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA ALA E 315 " pdb=" C ALA E 315 " pdb=" N PRO E 316 " pdb=" CA PRO E 316 " ideal model delta harmonic sigma weight residual 180.00 125.62 54.38 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 15095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3174 0.077 - 0.155: 627 0.155 - 0.232: 59 0.232 - 0.309: 1 0.309 - 0.387: 2 Chirality restraints: 3863 Sorted by residual: chirality pdb=" CB ILE B 595 " pdb=" CA ILE B 595 " pdb=" CG1 ILE B 595 " pdb=" CG2 ILE B 595 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB ILE B 417 " pdb=" CA ILE B 417 " pdb=" CG1 ILE B 417 " pdb=" CG2 ILE B 417 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CG LEU A 455 " pdb=" CB LEU A 455 " pdb=" CD1 LEU A 455 " pdb=" CD2 LEU A 455 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 3860 not shown) Planarity restraints: 4354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 315 " 0.065 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO E 316 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO E 316 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 316 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 228 " 0.032 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR E 228 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR E 228 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR E 228 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR E 228 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 228 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 228 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 228 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 102 " 0.058 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO B 103 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " 0.049 5.00e-02 4.00e+02 ... (remaining 4351 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4536 2.77 - 3.30: 22260 3.30 - 3.84: 38763 3.84 - 4.37: 44557 4.37 - 4.90: 76832 Nonbonded interactions: 186948 Sorted by model distance: nonbonded pdb=" OG1 THR C 430 " pdb=" OG SER F 222 " model vdw 2.240 3.040 nonbonded pdb=" O GLU A 48 " pdb=" OG1 THR A 51 " model vdw 2.265 3.040 nonbonded pdb=" O ILE A 531 " pdb=" OG1 THR A 535 " model vdw 2.278 3.040 nonbonded pdb=" NH2 ARG B 280 " pdb=" OE1 GLU B 387 " model vdw 2.290 3.120 nonbonded pdb=" O ILE D 328 " pdb=" OG SER D 332 " model vdw 2.290 3.040 ... (remaining 186943 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.950 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.600 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 : 0.010 0.559 24873 Z= 0.400 Angle : 1.228 42.720 33740 Z= 0.617 Chirality : 0.059 0.387 3863 Planarity : 0.008 0.099 4347 Dihedral : 9.843 80.473 9002 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.56 % Favored : 89.23 % Rotamer: Outliers : 0.16 % Allowed : 2.01 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 5.88 % Twisted General : 0.32 % 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: -4.22 (0.13), residues: 2870 helix: -2.47 (0.10), residues: 1393 sheet: -2.23 (0.28), residues: 300 loop : -3.25 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 616 TYR 0.068 0.004 TYR E 228 PHE 0.044 0.004 PHE A 451 TRP 0.048 0.004 TRP A 77 HIS 0.022 0.002 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00772 (24837) covalent geometry : angle 1.12554 (33672) SS BOND : bond 0.00669 ( 1) SS BOND : angle 2.82279 ( 2) hydrogen bonds : bond 0.15017 ( 1167) hydrogen bonds : angle 7.20036 ( 3384) metal coordination : bond 0.18875 ( 28) metal coordination : angle 13.46961 ( 45) link_TRANS : bond 0.00581 ( 7) link_TRANS : angle 1.95790 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 775 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8615 (mttt) cc_final: 0.8218 (mttm) REVERT: A 425 ARG cc_start: 0.7217 (ttt180) cc_final: 0.6182 (tmt170) REVERT: A 489 TYR cc_start: 0.7961 (t80) cc_final: 0.7131 (t80) REVERT: A 511 TRP cc_start: 0.6804 (m-10) cc_final: 0.5991 (m100) REVERT: A 564 ASN cc_start: 0.7787 (t0) cc_final: 0.7487 (t0) REVERT: A 679 PHE cc_start: 0.7282 (t80) cc_final: 0.6788 (t80) REVERT: A 715 LYS cc_start: 0.6796 (ttmt) cc_final: 0.6526 (ttpt) REVERT: B 32 LEU cc_start: 0.8261 (mp) cc_final: 0.7813 (tt) REVERT: B 42 MET cc_start: 0.8558 (tpp) cc_final: 0.8246 (tpt) REVERT: B 146 TYR cc_start: 0.8542 (t80) cc_final: 0.8038 (t80) REVERT: B 211 TYR cc_start: 0.8038 (t80) cc_final: 0.7167 (t80) REVERT: B 259 CYS cc_start: 0.7925 (t) cc_final: 0.7204 (t) REVERT: B 329 PHE cc_start: 0.8298 (t80) cc_final: 0.7886 (t80) REVERT: B 338 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6566 (mm-30) REVERT: B 478 MET cc_start: 0.8257 (tpp) cc_final: 0.7820 (ttp) REVERT: B 505 SER cc_start: 0.8625 (p) cc_final: 0.8395 (t) REVERT: B 520 TYR cc_start: 0.7835 (m-80) cc_final: 0.7594 (m-80) REVERT: B 620 MET cc_start: 0.7927 (tpp) cc_final: 0.7552 (mmm) REVERT: C 216 THR cc_start: 0.7668 (m) cc_final: 0.7454 (t) REVERT: C 346 GLN cc_start: 0.5094 (mt0) cc_final: 0.4623 (pm20) REVERT: C 384 HIS cc_start: 0.7047 (p-80) cc_final: 0.6653 (p-80) REVERT: C 473 ARG cc_start: 0.7359 (ttt180) cc_final: 0.7048 (tmt170) REVERT: C 474 HIS cc_start: 0.5365 (m-70) cc_final: 0.5144 (m170) REVERT: C 527 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6720 (tp30) REVERT: D 140 LYS cc_start: 0.7989 (mttt) cc_final: 0.7704 (tmtt) REVERT: D 173 GLN cc_start: 0.7849 (pt0) cc_final: 0.7495 (tm-30) REVERT: D 215 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7832 (t80) REVERT: D 247 LYS cc_start: 0.7116 (mttt) cc_final: 0.6275 (pttp) REVERT: D 249 TYR cc_start: 0.6387 (m-80) cc_final: 0.6107 (m-80) REVERT: D 268 PHE cc_start: 0.8213 (m-10) cc_final: 0.7946 (m-80) REVERT: E 66 ASP cc_start: 0.8558 (m-30) cc_final: 0.8247 (m-30) REVERT: E 138 THR cc_start: 0.8363 (m) cc_final: 0.8159 (m) REVERT: E 229 LYS cc_start: 0.8306 (mttt) cc_final: 0.8050 (mttm) REVERT: E 249 LEU cc_start: 0.8871 (tp) cc_final: 0.8299 (mp) REVERT: E 306 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7366 (pttm) REVERT: F 133 LEU cc_start: 0.8682 (tp) cc_final: 0.8358 (mm) REVERT: F 266 TYR cc_start: 0.8172 (m-80) cc_final: 0.7806 (m-80) REVERT: G 24 ASP cc_start: 0.7121 (t70) cc_final: 0.6920 (t0) REVERT: H 108 ASN cc_start: 0.7515 (m-40) cc_final: 0.7014 (m110) REVERT: H 155 ARG cc_start: 0.7568 (mtt180) cc_final: 0.6993 (ttp80) REVERT: H 168 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7591 (mt-10) REVERT: H 171 LEU cc_start: 0.8410 (tp) cc_final: 0.8159 (tt) outliers start: 4 outliers final: 2 residues processed: 778 average time/residue: 0.1947 time to fit residues: 222.1260 Evaluate side-chains 414 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 411 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain F residue 157 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0770 chunk 111 optimal weight: 4.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 HIS B 164 HIS B 237 HIS D 18 ASN D 54 ASN D 116 GLN D 141 HIS D 181 GLN D 289 ASN D 302 HIS ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 235 HIS E 257 HIS ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN F 225 GLN G 36 GLN G 64 ASN H 28 HIS H 117 ASN H 136 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.150597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.124298 restraints weight = 44185.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.126990 restraints weight = 27009.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128403 restraints weight = 18357.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.128669 restraints weight = 15242.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128834 restraints weight = 14065.590| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 2.195 24873 Z= 0.286 Angle : 0.759 21.510 33740 Z= 0.366 Chirality : 0.043 0.206 3863 Planarity : 0.005 0.084 4347 Dihedral : 6.460 73.560 3432 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.90 % Favored : 93.03 % Rotamer: Outliers : 2.77 % Allowed : 10.53 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 3.36 % Twisted General : 0.14 % 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: -2.61 (0.14), residues: 2870 helix: -0.71 (0.13), residues: 1415 sheet: -2.00 (0.28), residues: 303 loop : -2.94 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 639 TYR 0.039 0.002 TYR A 581 PHE 0.024 0.002 PHE C 225 TRP 0.022 0.002 TRP A 493 HIS 0.007 0.001 HIS D 424 Details of bonding type rmsd covalent geometry : bond 0.00307 (24837) covalent geometry : angle 0.70204 (33672) SS BOND : bond 0.00911 ( 1) SS BOND : angle 3.96975 ( 2) hydrogen bonds : bond 0.04431 ( 1167) hydrogen bonds : angle 5.09158 ( 3384) metal coordination : bond 0.41494 ( 28) metal coordination : angle 7.86705 ( 45) link_TRANS : bond 0.00191 ( 7) link_TRANS : angle 0.71715 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 530 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8566 (mttt) cc_final: 0.8366 (mtmm) REVERT: A 291 LEU cc_start: 0.7007 (mt) cc_final: 0.6695 (mt) REVERT: A 399 LYS cc_start: 0.7522 (mmmm) cc_final: 0.6987 (mmtm) REVERT: A 425 ARG cc_start: 0.7309 (ttt180) cc_final: 0.6187 (tmt170) REVERT: A 429 TRP cc_start: 0.7504 (t60) cc_final: 0.6955 (t-100) REVERT: A 506 GLN cc_start: 0.7536 (tp40) cc_final: 0.7062 (mm110) REVERT: A 529 LYS cc_start: 0.8103 (tttt) cc_final: 0.7671 (mttp) REVERT: A 561 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6761 (m-10) REVERT: A 564 ASN cc_start: 0.8120 (t0) cc_final: 0.7810 (t0) REVERT: A 639 ARG cc_start: 0.8094 (ptp-170) cc_final: 0.7736 (mtp-110) REVERT: A 655 TYR cc_start: 0.7349 (m-80) cc_final: 0.6847 (m-80) REVERT: A 715 LYS cc_start: 0.6478 (ttmt) cc_final: 0.6249 (ttpt) REVERT: B 25 MET cc_start: 0.7915 (mmm) cc_final: 0.7384 (mmt) REVERT: B 42 MET cc_start: 0.8416 (tpp) cc_final: 0.7840 (tpt) REVERT: B 211 TYR cc_start: 0.7950 (t80) cc_final: 0.7239 (t80) REVERT: B 220 LEU cc_start: 0.4533 (OUTLIER) cc_final: 0.4277 (pp) REVERT: B 274 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7830 (tptp) REVERT: B 338 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6467 (mm-30) REVERT: B 421 PHE cc_start: 0.7459 (p90) cc_final: 0.6898 (p90) REVERT: B 478 MET cc_start: 0.8276 (tpp) cc_final: 0.7997 (ttp) REVERT: B 629 GLN cc_start: 0.6524 (tp-100) cc_final: 0.5314 (tt0) REVERT: B 751 LYS cc_start: 0.7295 (mttt) cc_final: 0.6951 (mmtt) REVERT: C 313 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6624 (mmt) REVERT: C 346 GLN cc_start: 0.4989 (mt0) cc_final: 0.4735 (pt0) REVERT: C 380 ASP cc_start: 0.7318 (t70) cc_final: 0.7064 (t70) REVERT: C 527 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6978 (tp30) REVERT: D 57 MET cc_start: 0.8109 (tpp) cc_final: 0.7815 (tpp) REVERT: D 140 LYS cc_start: 0.8000 (mttt) cc_final: 0.7722 (tmtt) REVERT: D 247 LYS cc_start: 0.7147 (mttt) cc_final: 0.6377 (pttp) REVERT: D 268 PHE cc_start: 0.8142 (m-10) cc_final: 0.7753 (m-10) REVERT: D 418 PHE cc_start: 0.6509 (t80) cc_final: 0.5674 (t80) REVERT: D 433 PHE cc_start: 0.6268 (t80) cc_final: 0.5953 (t80) REVERT: E 66 ASP cc_start: 0.8266 (m-30) cc_final: 0.8010 (m-30) REVERT: E 74 GLN cc_start: 0.7730 (mt0) cc_final: 0.7449 (mm110) REVERT: E 175 THR cc_start: 0.9158 (m) cc_final: 0.8896 (p) REVERT: E 249 LEU cc_start: 0.8837 (tp) cc_final: 0.8629 (mm) REVERT: E 306 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7129 (pttm) REVERT: E 331 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6955 (m-10) REVERT: F 8 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7838 (tp) REVERT: F 116 LYS cc_start: 0.8505 (mttt) cc_final: 0.8070 (mmmt) REVERT: F 133 LEU cc_start: 0.8092 (tp) cc_final: 0.7873 (tt) REVERT: F 160 ARG cc_start: 0.8490 (ptt90) cc_final: 0.8247 (ptt90) REVERT: H 71 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7838 (pt0) REVERT: H 154 GLU cc_start: 0.7987 (tt0) cc_final: 0.7505 (tp30) REVERT: H 155 ARG cc_start: 0.7617 (mtt180) cc_final: 0.7058 (ttp80) REVERT: H 168 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7392 (mt-10) REVERT: H 169 GLU cc_start: 0.7525 (pt0) cc_final: 0.7279 (pp20) REVERT: H 171 LEU cc_start: 0.8156 (tp) cc_final: 0.7950 (tt) outliers start: 69 outliers final: 31 residues processed: 571 average time/residue: 0.1683 time to fit residues: 148.4447 Evaluate side-chains 423 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 386 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 113 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 103 optimal weight: 6.9990 chunk 129 optimal weight: 0.0010 chunk 153 optimal weight: 0.7980 chunk 251 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 255 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN D 181 GLN D 312 ASN D 390 GLN E 140 HIS ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.149667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123729 restraints weight = 44292.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125979 restraints weight = 28359.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.127388 restraints weight = 20009.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127647 restraints weight = 16280.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.127847 restraints weight = 15350.385| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.167 24873 Z= 0.139 Angle : 0.719 21.331 33740 Z= 0.343 Chirality : 0.043 0.276 3863 Planarity : 0.005 0.076 4347 Dihedral : 5.885 69.309 3427 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.44 % Rotamer: Outliers : 3.14 % Allowed : 13.06 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.11 % 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: -1.87 (0.15), residues: 2870 helix: 0.11 (0.13), residues: 1411 sheet: -1.94 (0.28), residues: 326 loop : -2.79 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 282 TYR 0.027 0.002 TYR A 581 PHE 0.035 0.002 PHE D 331 TRP 0.013 0.002 TRP A 493 HIS 0.036 0.001 HIS H 28 Details of bonding type rmsd covalent geometry : bond 0.00306 (24837) covalent geometry : angle 0.66347 (33672) SS BOND : bond 0.01219 ( 1) SS BOND : angle 4.99815 ( 2) hydrogen bonds : bond 0.04063 ( 1167) hydrogen bonds : angle 4.76374 ( 3384) metal coordination : bond 0.03268 ( 28) metal coordination : angle 7.56723 ( 45) link_TRANS : bond 0.00169 ( 7) link_TRANS : angle 0.51594 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 457 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8574 (mttt) cc_final: 0.8336 (mttm) REVERT: A 291 LEU cc_start: 0.6901 (mt) cc_final: 0.6587 (mt) REVERT: A 309 ASP cc_start: 0.7813 (t0) cc_final: 0.7560 (t0) REVERT: A 399 LYS cc_start: 0.7552 (mmmm) cc_final: 0.7235 (mmtm) REVERT: A 425 ARG cc_start: 0.6951 (ttt180) cc_final: 0.5944 (tmt170) REVERT: A 429 TRP cc_start: 0.7387 (t60) cc_final: 0.6801 (t-100) REVERT: A 489 TYR cc_start: 0.7932 (t80) cc_final: 0.7687 (t80) REVERT: A 506 GLN cc_start: 0.7611 (tp40) cc_final: 0.7397 (mm110) REVERT: A 528 LYS cc_start: 0.8432 (ptpp) cc_final: 0.7918 (mmtt) REVERT: A 529 LYS cc_start: 0.8172 (tttt) cc_final: 0.7722 (mttp) REVERT: A 561 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6583 (m-10) REVERT: A 564 ASN cc_start: 0.8039 (t0) cc_final: 0.7755 (t0) REVERT: A 639 ARG cc_start: 0.7971 (ptp-170) cc_final: 0.7494 (mtp-110) REVERT: A 655 TYR cc_start: 0.7337 (m-80) cc_final: 0.6752 (m-80) REVERT: B 42 MET cc_start: 0.8126 (tpp) cc_final: 0.7681 (tpt) REVERT: B 211 TYR cc_start: 0.7999 (t80) cc_final: 0.7271 (t80) REVERT: B 220 LEU cc_start: 0.4516 (OUTLIER) cc_final: 0.4275 (pp) REVERT: B 274 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7756 (tptp) REVERT: B 338 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6331 (mm-30) REVERT: B 421 PHE cc_start: 0.7403 (p90) cc_final: 0.6910 (p90) REVERT: B 542 TYR cc_start: 0.7250 (m-80) cc_final: 0.7048 (m-80) REVERT: B 629 GLN cc_start: 0.6486 (tp-100) cc_final: 0.5350 (tt0) REVERT: C 230 PHE cc_start: 0.7501 (t80) cc_final: 0.7301 (t80) REVERT: C 313 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6625 (mmt) REVERT: C 346 GLN cc_start: 0.4953 (mt0) cc_final: 0.4676 (pt0) REVERT: C 527 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6957 (tp30) REVERT: D 54 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8062 (t160) REVERT: D 57 MET cc_start: 0.8206 (tpp) cc_final: 0.7901 (tpp) REVERT: D 140 LYS cc_start: 0.7934 (mttt) cc_final: 0.7722 (tmtt) REVERT: D 247 LYS cc_start: 0.6919 (mttt) cc_final: 0.6234 (ptmm) REVERT: D 268 PHE cc_start: 0.8157 (m-10) cc_final: 0.7791 (m-80) REVERT: D 418 PHE cc_start: 0.6862 (t80) cc_final: 0.6346 (t80) REVERT: E 62 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7903 (t80) REVERT: E 74 GLN cc_start: 0.7714 (mt0) cc_final: 0.7503 (mm110) REVERT: E 249 LEU cc_start: 0.8830 (tp) cc_final: 0.8404 (mp) REVERT: F 160 ARG cc_start: 0.8584 (ptt90) cc_final: 0.8238 (ptt90) REVERT: G 43 VAL cc_start: 0.7008 (OUTLIER) cc_final: 0.6672 (p) REVERT: H 154 GLU cc_start: 0.7913 (tt0) cc_final: 0.7421 (tp30) REVERT: H 155 ARG cc_start: 0.7375 (mtt180) cc_final: 0.6902 (ttp80) REVERT: H 168 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7403 (mt-10) outliers start: 78 outliers final: 46 residues processed: 510 average time/residue: 0.1596 time to fit residues: 127.5991 Evaluate side-chains 437 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 384 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 186 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 121 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 144 optimal weight: 9.9990 chunk 135 optimal weight: 0.3980 chunk 279 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN E 140 HIS ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.153179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127422 restraints weight = 44076.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.128766 restraints weight = 28887.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.130344 restraints weight = 21575.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.130892 restraints weight = 17476.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130981 restraints weight = 15980.898| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 24873 Z= 0.123 Angle : 0.685 19.654 33740 Z= 0.326 Chirality : 0.042 0.271 3863 Planarity : 0.004 0.073 4347 Dihedral : 5.441 61.738 3427 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.90 % Favored : 93.07 % Rotamer: Outliers : 3.14 % Allowed : 14.99 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.15), residues: 2870 helix: 0.57 (0.14), residues: 1428 sheet: -1.85 (0.28), residues: 321 loop : -2.66 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 371 TYR 0.035 0.001 TYR A 581 PHE 0.028 0.002 PHE D 331 TRP 0.015 0.001 TRP A 493 HIS 0.016 0.001 HIS H 28 Details of bonding type rmsd covalent geometry : bond 0.00272 (24837) covalent geometry : angle 0.64444 (33672) SS BOND : bond 0.00838 ( 1) SS BOND : angle 4.62698 ( 2) hydrogen bonds : bond 0.03737 ( 1167) hydrogen bonds : angle 4.52013 ( 3384) metal coordination : bond 0.02673 ( 28) metal coordination : angle 6.28839 ( 45) link_TRANS : bond 0.00170 ( 7) link_TRANS : angle 0.46552 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 445 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8556 (mttt) cc_final: 0.8314 (mttm) REVERT: A 291 LEU cc_start: 0.6899 (mt) cc_final: 0.6627 (mt) REVERT: A 309 ASP cc_start: 0.7758 (t0) cc_final: 0.7536 (t0) REVERT: A 399 LYS cc_start: 0.7495 (mmmm) cc_final: 0.7259 (mmtm) REVERT: A 425 ARG cc_start: 0.6905 (ttt180) cc_final: 0.6030 (tmt170) REVERT: A 528 LYS cc_start: 0.8389 (ptpp) cc_final: 0.7840 (ttmm) REVERT: A 529 LYS cc_start: 0.8150 (tttt) cc_final: 0.7712 (mttp) REVERT: A 561 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6564 (m-10) REVERT: A 639 ARG cc_start: 0.7964 (ptp-170) cc_final: 0.7528 (mtp-110) REVERT: A 650 MET cc_start: 0.5968 (mtp) cc_final: 0.5537 (ttm) REVERT: A 655 TYR cc_start: 0.7347 (m-80) cc_final: 0.6916 (m-80) REVERT: B 25 MET cc_start: 0.7325 (mmm) cc_final: 0.7037 (mmt) REVERT: B 42 MET cc_start: 0.8023 (tpp) cc_final: 0.7640 (tpt) REVERT: B 211 TYR cc_start: 0.7998 (t80) cc_final: 0.7279 (t80) REVERT: B 329 PHE cc_start: 0.7986 (t80) cc_final: 0.7467 (t80) REVERT: B 338 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6317 (mm-30) REVERT: B 421 PHE cc_start: 0.7418 (p90) cc_final: 0.6908 (p90) REVERT: B 542 TYR cc_start: 0.7339 (m-80) cc_final: 0.7081 (m-80) REVERT: B 629 GLN cc_start: 0.6566 (tp-100) cc_final: 0.5365 (tt0) REVERT: B 633 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8108 (mt) REVERT: C 226 GLN cc_start: 0.6938 (pt0) cc_final: 0.6230 (pt0) REVERT: C 313 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6654 (mmt) REVERT: C 346 GLN cc_start: 0.4918 (mt0) cc_final: 0.4398 (pm20) REVERT: C 524 HIS cc_start: 0.7443 (t-170) cc_final: 0.7204 (t-170) REVERT: D 37 HIS cc_start: 0.6804 (OUTLIER) cc_final: 0.6294 (t-90) REVERT: D 161 HIS cc_start: 0.8086 (m170) cc_final: 0.7759 (m170) REVERT: D 247 LYS cc_start: 0.6731 (mttt) cc_final: 0.6179 (ptmm) REVERT: D 268 PHE cc_start: 0.8034 (m-10) cc_final: 0.7718 (m-80) REVERT: D 418 PHE cc_start: 0.6776 (t80) cc_final: 0.6143 (t80) REVERT: E 74 GLN cc_start: 0.7631 (mt0) cc_final: 0.7259 (mm-40) REVERT: E 249 LEU cc_start: 0.8799 (tp) cc_final: 0.8388 (mp) REVERT: E 331 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6764 (m-10) REVERT: F 160 ARG cc_start: 0.8562 (ptt90) cc_final: 0.8235 (ptt90) REVERT: F 213 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7252 (tt) REVERT: G 43 VAL cc_start: 0.6942 (OUTLIER) cc_final: 0.6695 (p) REVERT: H 154 GLU cc_start: 0.7948 (tt0) cc_final: 0.7628 (tp30) REVERT: H 155 ARG cc_start: 0.7244 (mtt180) cc_final: 0.6839 (ttp80) REVERT: H 171 LEU cc_start: 0.8061 (tt) cc_final: 0.7764 (mm) outliers start: 78 outliers final: 39 residues processed: 500 average time/residue: 0.1581 time to fit residues: 125.4150 Evaluate side-chains 428 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 382 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 357 SER Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 111 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 109 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 253 optimal weight: 9.9990 chunk 97 optimal weight: 0.0000 chunk 257 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 HIS B 241 ASN D 54 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.147559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.120933 restraints weight = 44673.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123299 restraints weight = 29432.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.124422 restraints weight = 20672.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.124870 restraints weight = 17571.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125037 restraints weight = 16486.334| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 24873 Z= 0.206 Angle : 0.757 23.159 33740 Z= 0.363 Chirality : 0.045 0.305 3863 Planarity : 0.005 0.074 4347 Dihedral : 5.629 55.183 3427 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.54 % Favored : 91.43 % Rotamer: Outliers : 3.98 % Allowed : 15.68 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.15), residues: 2870 helix: 0.59 (0.14), residues: 1425 sheet: -1.95 (0.28), residues: 320 loop : -2.67 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 371 TYR 0.025 0.002 TYR A 581 PHE 0.031 0.002 PHE D 331 TRP 0.026 0.002 TRP A 511 HIS 0.009 0.001 HIS H 28 Details of bonding type rmsd covalent geometry : bond 0.00478 (24837) covalent geometry : angle 0.70780 (33672) SS BOND : bond 0.00715 ( 1) SS BOND : angle 4.66574 ( 2) hydrogen bonds : bond 0.04220 ( 1167) hydrogen bonds : angle 4.71613 ( 3384) metal coordination : bond 0.01914 ( 28) metal coordination : angle 7.31057 ( 45) link_TRANS : bond 0.00148 ( 7) link_TRANS : angle 0.50277 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 404 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8687 (mttt) cc_final: 0.8419 (mttm) REVERT: A 291 LEU cc_start: 0.6645 (mt) cc_final: 0.6373 (mt) REVERT: A 399 LYS cc_start: 0.7599 (mmmm) cc_final: 0.7277 (mmtm) REVERT: A 425 ARG cc_start: 0.7123 (ttt180) cc_final: 0.6134 (tmt170) REVERT: A 528 LYS cc_start: 0.8368 (ptpp) cc_final: 0.7806 (ttmm) REVERT: A 529 LYS cc_start: 0.8153 (tttt) cc_final: 0.7723 (mttp) REVERT: A 561 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6611 (m-10) REVERT: A 639 ARG cc_start: 0.7904 (ptp-170) cc_final: 0.7511 (mtp180) REVERT: A 650 MET cc_start: 0.6065 (mtp) cc_final: 0.5524 (ttm) REVERT: B 42 MET cc_start: 0.8043 (tpp) cc_final: 0.7684 (tpt) REVERT: B 211 TYR cc_start: 0.8282 (t80) cc_final: 0.7408 (t80) REVERT: B 274 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7816 (tptp) REVERT: B 338 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6274 (mm-30) REVERT: B 421 PHE cc_start: 0.7545 (p90) cc_final: 0.7262 (p90) REVERT: B 629 GLN cc_start: 0.6355 (tp-100) cc_final: 0.5226 (tt0) REVERT: C 313 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6673 (mmt) REVERT: C 346 GLN cc_start: 0.4968 (mt0) cc_final: 0.4394 (pm20) REVERT: C 405 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7961 (mp10) REVERT: C 473 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7641 (ttp80) REVERT: D 37 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6362 (t-90) REVERT: D 54 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8125 (t160) REVERT: D 247 LYS cc_start: 0.6779 (mttt) cc_final: 0.6246 (ptmm) REVERT: D 268 PHE cc_start: 0.8288 (m-10) cc_final: 0.7900 (m-80) REVERT: D 418 PHE cc_start: 0.6849 (t80) cc_final: 0.6346 (t80) REVERT: E 74 GLN cc_start: 0.7732 (mt0) cc_final: 0.7381 (mm-40) REVERT: E 249 LEU cc_start: 0.8794 (tp) cc_final: 0.8302 (mp) REVERT: E 331 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6753 (m-10) REVERT: F 133 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7265 (tt) REVERT: F 213 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7451 (tt) REVERT: G 5 LEU cc_start: 0.4773 (OUTLIER) cc_final: 0.4432 (tt) REVERT: G 41 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.7174 (m) REVERT: H 108 ASN cc_start: 0.7472 (m-40) cc_final: 0.6909 (m110) REVERT: H 155 ARG cc_start: 0.7218 (mtt180) cc_final: 0.6727 (ttp80) outliers start: 99 outliers final: 61 residues processed: 483 average time/residue: 0.1573 time to fit residues: 120.3203 Evaluate side-chains 433 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 361 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 186 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 53 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 209 optimal weight: 4.9990 chunk 264 optimal weight: 30.0000 chunk 132 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN F 173 GLN ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.148251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.121856 restraints weight = 44388.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124051 restraints weight = 28970.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125268 restraints weight = 20567.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125739 restraints weight = 17006.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.125851 restraints weight = 16078.177| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24873 Z= 0.152 Angle : 0.701 20.900 33740 Z= 0.334 Chirality : 0.043 0.255 3863 Planarity : 0.004 0.072 4347 Dihedral : 5.401 58.252 3427 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.39 % Favored : 92.58 % Rotamer: Outliers : 3.94 % Allowed : 16.64 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.16), residues: 2870 helix: 0.80 (0.14), residues: 1424 sheet: -1.90 (0.28), residues: 318 loop : -2.58 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 371 TYR 0.023 0.002 TYR A 534 PHE 0.029 0.002 PHE D 331 TRP 0.023 0.002 TRP A 511 HIS 0.010 0.001 HIS C 524 Details of bonding type rmsd covalent geometry : bond 0.00348 (24837) covalent geometry : angle 0.65419 (33672) SS BOND : bond 0.00706 ( 1) SS BOND : angle 4.39112 ( 2) hydrogen bonds : bond 0.03831 ( 1167) hydrogen bonds : angle 4.54913 ( 3384) metal coordination : bond 0.01547 ( 28) metal coordination : angle 6.87661 ( 45) link_TRANS : bond 0.00151 ( 7) link_TRANS : angle 0.49851 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 381 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8649 (mttt) cc_final: 0.8360 (mttm) REVERT: A 399 LYS cc_start: 0.7529 (mmmm) cc_final: 0.7250 (mmtm) REVERT: A 425 ARG cc_start: 0.7072 (ttt180) cc_final: 0.6124 (tmt170) REVERT: A 511 TRP cc_start: 0.6744 (m-10) cc_final: 0.6375 (m-90) REVERT: A 528 LYS cc_start: 0.8350 (ptpp) cc_final: 0.7941 (ttmm) REVERT: A 529 LYS cc_start: 0.8146 (tttt) cc_final: 0.7719 (mttp) REVERT: A 561 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6570 (m-10) REVERT: A 639 ARG cc_start: 0.7877 (ptp-170) cc_final: 0.7479 (mtp180) REVERT: A 650 MET cc_start: 0.5998 (mtp) cc_final: 0.5649 (ttm) REVERT: B 25 MET cc_start: 0.7479 (mmm) cc_final: 0.7122 (mmt) REVERT: B 42 MET cc_start: 0.8111 (tpp) cc_final: 0.7905 (tpt) REVERT: B 274 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7793 (tptp) REVERT: B 329 PHE cc_start: 0.7985 (t80) cc_final: 0.7686 (t80) REVERT: B 338 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6171 (mm-30) REVERT: B 421 PHE cc_start: 0.7657 (p90) cc_final: 0.7407 (p90) REVERT: B 542 TYR cc_start: 0.7515 (m-80) cc_final: 0.7231 (m-80) REVERT: B 629 GLN cc_start: 0.6234 (tp-100) cc_final: 0.5222 (tt0) REVERT: C 226 GLN cc_start: 0.7022 (pt0) cc_final: 0.6309 (pt0) REVERT: C 313 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6625 (mmt) REVERT: C 346 GLN cc_start: 0.4945 (mt0) cc_final: 0.4374 (pm20) REVERT: D 58 ARG cc_start: 0.7714 (tpt170) cc_final: 0.7470 (tpt170) REVERT: D 247 LYS cc_start: 0.6767 (mttt) cc_final: 0.6198 (ptmm) REVERT: D 268 PHE cc_start: 0.8234 (m-10) cc_final: 0.7868 (m-80) REVERT: D 398 ARG cc_start: 0.6342 (tpt170) cc_final: 0.5727 (tpp-160) REVERT: D 418 PHE cc_start: 0.6842 (t80) cc_final: 0.6017 (t80) REVERT: E 74 GLN cc_start: 0.7858 (mt0) cc_final: 0.7493 (mm-40) REVERT: E 119 GLU cc_start: 0.6963 (mp0) cc_final: 0.6748 (mp0) REVERT: E 249 LEU cc_start: 0.8735 (tp) cc_final: 0.8411 (mp) REVERT: E 331 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6696 (m-10) REVERT: F 150 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7433 (mt-10) REVERT: F 153 ASP cc_start: 0.7733 (m-30) cc_final: 0.7531 (m-30) REVERT: F 213 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7339 (tt) REVERT: H 71 GLU cc_start: 0.8016 (tt0) cc_final: 0.7223 (tm-30) REVERT: H 155 ARG cc_start: 0.7353 (mtt180) cc_final: 0.6734 (ttp80) outliers start: 98 outliers final: 63 residues processed: 460 average time/residue: 0.1627 time to fit residues: 119.2125 Evaluate side-chains 426 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 358 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 7 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 186 optimal weight: 0.0570 chunk 63 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.147060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120978 restraints weight = 44423.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122865 restraints weight = 29349.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124267 restraints weight = 20672.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124608 restraints weight = 17399.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124624 restraints weight = 15983.083| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 24873 Z= 0.174 Angle : 0.716 21.779 33740 Z= 0.342 Chirality : 0.044 0.274 3863 Planarity : 0.004 0.072 4347 Dihedral : 5.421 56.822 3427 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.40 % Favored : 91.57 % Rotamer: Outliers : 3.86 % Allowed : 16.80 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.16), residues: 2870 helix: 0.87 (0.14), residues: 1419 sheet: -1.91 (0.28), residues: 324 loop : -2.53 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 439 TYR 0.023 0.002 TYR F 101 PHE 0.029 0.002 PHE D 331 TRP 0.020 0.002 TRP D 129 HIS 0.009 0.001 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00404 (24837) covalent geometry : angle 0.67106 (33672) SS BOND : bond 0.00664 ( 1) SS BOND : angle 4.24599 ( 2) hydrogen bonds : bond 0.03952 ( 1167) hydrogen bonds : angle 4.55970 ( 3384) metal coordination : bond 0.01411 ( 28) metal coordination : angle 6.82465 ( 45) link_TRANS : bond 0.00151 ( 7) link_TRANS : angle 0.50901 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 378 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8627 (mttt) cc_final: 0.8369 (mttm) REVERT: A 399 LYS cc_start: 0.7574 (mmmm) cc_final: 0.7269 (mmtm) REVERT: A 425 ARG cc_start: 0.7098 (ttt180) cc_final: 0.6138 (tmt170) REVERT: A 528 LYS cc_start: 0.8346 (ptpp) cc_final: 0.7937 (ttmm) REVERT: A 529 LYS cc_start: 0.8089 (tttt) cc_final: 0.7724 (mttp) REVERT: A 536 MET cc_start: 0.5492 (mmm) cc_final: 0.5277 (mmm) REVERT: A 561 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6732 (m-10) REVERT: A 639 ARG cc_start: 0.7874 (ptp-170) cc_final: 0.7505 (mtp180) REVERT: A 650 MET cc_start: 0.5991 (mtp) cc_final: 0.5670 (ttm) REVERT: B 25 MET cc_start: 0.7579 (mmm) cc_final: 0.7289 (mmp) REVERT: B 274 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7802 (tptp) REVERT: B 338 GLU cc_start: 0.6638 (mm-30) cc_final: 0.6142 (mm-30) REVERT: B 421 PHE cc_start: 0.7660 (p90) cc_final: 0.7184 (p90) REVERT: B 629 GLN cc_start: 0.6196 (tp-100) cc_final: 0.5247 (tt0) REVERT: B 751 LYS cc_start: 0.7297 (mttt) cc_final: 0.7006 (mmtt) REVERT: C 226 GLN cc_start: 0.7174 (pt0) cc_final: 0.6475 (pt0) REVERT: C 313 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6643 (mmt) REVERT: C 346 GLN cc_start: 0.4903 (mt0) cc_final: 0.4473 (pm20) REVERT: C 405 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: C 528 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6351 (mtt) REVERT: D 37 HIS cc_start: 0.7074 (OUTLIER) cc_final: 0.6447 (t-90) REVERT: D 115 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6769 (ttm170) REVERT: D 247 LYS cc_start: 0.6714 (mttt) cc_final: 0.6165 (ptmm) REVERT: D 268 PHE cc_start: 0.8257 (m-10) cc_final: 0.7892 (m-80) REVERT: D 433 PHE cc_start: 0.6150 (t80) cc_final: 0.5929 (t80) REVERT: E 249 LEU cc_start: 0.8744 (tp) cc_final: 0.8397 (mp) REVERT: E 331 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6708 (m-10) REVERT: F 150 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7596 (mt-10) REVERT: F 213 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7424 (tt) REVERT: H 71 GLU cc_start: 0.8092 (tt0) cc_final: 0.7299 (tm-30) REVERT: H 108 ASN cc_start: 0.7723 (m-40) cc_final: 0.7256 (m110) REVERT: H 155 ARG cc_start: 0.7530 (mtt180) cc_final: 0.6873 (ttp80) outliers start: 96 outliers final: 72 residues processed: 451 average time/residue: 0.1499 time to fit residues: 108.6209 Evaluate side-chains 435 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 354 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 142 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 224 optimal weight: 0.1980 chunk 211 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 162 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 345 GLN ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.150249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.124275 restraints weight = 44233.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126593 restraints weight = 28121.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.127939 restraints weight = 19855.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128155 restraints weight = 16413.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128291 restraints weight = 15583.114| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24873 Z= 0.127 Angle : 0.676 19.365 33740 Z= 0.324 Chirality : 0.042 0.277 3863 Planarity : 0.004 0.072 4347 Dihedral : 5.178 55.757 3427 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.25 % Favored : 92.72 % Rotamer: Outliers : 3.46 % Allowed : 17.93 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.16), residues: 2870 helix: 1.07 (0.14), residues: 1419 sheet: -1.74 (0.28), residues: 324 loop : -2.44 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 378 TYR 0.022 0.001 TYR A 534 PHE 0.030 0.002 PHE D 331 TRP 0.024 0.001 TRP A 493 HIS 0.010 0.001 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00287 (24837) covalent geometry : angle 0.63684 (33672) SS BOND : bond 0.00635 ( 1) SS BOND : angle 4.03595 ( 2) hydrogen bonds : bond 0.03670 ( 1167) hydrogen bonds : angle 4.42765 ( 3384) metal coordination : bond 0.01214 ( 28) metal coordination : angle 6.18023 ( 45) link_TRANS : bond 0.00163 ( 7) link_TRANS : angle 0.49024 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 402 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8605 (mttt) cc_final: 0.8319 (mttm) REVERT: A 325 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7613 (ttm170) REVERT: A 378 PHE cc_start: 0.8513 (t80) cc_final: 0.8277 (t80) REVERT: A 380 MET cc_start: 0.7698 (tpp) cc_final: 0.7477 (tpp) REVERT: A 399 LYS cc_start: 0.7426 (mmmm) cc_final: 0.7179 (mmtm) REVERT: A 425 ARG cc_start: 0.7008 (ttt180) cc_final: 0.6131 (tmt170) REVERT: A 495 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: A 529 LYS cc_start: 0.8042 (tttt) cc_final: 0.7804 (mttp) REVERT: A 561 PHE cc_start: 0.7007 (OUTLIER) cc_final: 0.6732 (m-10) REVERT: A 621 ASN cc_start: 0.7486 (m110) cc_final: 0.7116 (t0) REVERT: A 639 ARG cc_start: 0.7970 (ptp-170) cc_final: 0.7493 (mtp180) REVERT: A 650 MET cc_start: 0.5737 (mtp) cc_final: 0.5422 (ttm) REVERT: B 25 MET cc_start: 0.7452 (mmm) cc_final: 0.7168 (mmt) REVERT: B 338 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6235 (mm-30) REVERT: B 421 PHE cc_start: 0.7653 (p90) cc_final: 0.7160 (p90) REVERT: B 527 MET cc_start: 0.8504 (tpp) cc_final: 0.8112 (tpp) REVERT: B 542 TYR cc_start: 0.7490 (m-80) cc_final: 0.7212 (m-80) REVERT: B 629 GLN cc_start: 0.6068 (tp-100) cc_final: 0.5242 (tt0) REVERT: C 226 GLN cc_start: 0.6996 (pt0) cc_final: 0.6379 (pt0) REVERT: C 313 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6604 (mmt) REVERT: C 346 GLN cc_start: 0.4841 (mt0) cc_final: 0.4438 (pm20) REVERT: D 115 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6725 (ttm170) REVERT: D 247 LYS cc_start: 0.6678 (mttt) cc_final: 0.6155 (ptmm) REVERT: D 268 PHE cc_start: 0.8211 (m-10) cc_final: 0.7913 (m-80) REVERT: D 433 PHE cc_start: 0.6193 (t80) cc_final: 0.5967 (t80) REVERT: E 249 LEU cc_start: 0.8736 (tp) cc_final: 0.8435 (mp) REVERT: E 308 CYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8399 (m) REVERT: E 331 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6611 (m-10) REVERT: F 150 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7617 (mt-10) REVERT: F 213 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7309 (tt) REVERT: F 251 TYR cc_start: 0.7222 (m-10) cc_final: 0.6820 (m-10) REVERT: H 71 GLU cc_start: 0.8093 (tt0) cc_final: 0.7207 (tm-30) REVERT: H 155 ARG cc_start: 0.7465 (mtt180) cc_final: 0.6942 (ttp80) outliers start: 86 outliers final: 62 residues processed: 468 average time/residue: 0.1540 time to fit residues: 115.0950 Evaluate side-chains 428 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 359 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 308 CYS Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 186 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 139 optimal weight: 0.4980 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN F 108 ASN ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.141975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115268 restraints weight = 45392.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117493 restraints weight = 30279.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.118743 restraints weight = 20985.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119089 restraints weight = 18237.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118942 restraints weight = 16782.464| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 24873 Z= 0.267 Angle : 0.829 27.600 33740 Z= 0.398 Chirality : 0.048 0.244 3863 Planarity : 0.005 0.077 4347 Dihedral : 5.743 57.043 3427 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.44 % Favored : 90.52 % Rotamer: Outliers : 3.54 % Allowed : 18.45 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 2870 helix: 0.59 (0.14), residues: 1431 sheet: -1.83 (0.29), residues: 298 loop : -2.56 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 439 TYR 0.022 0.002 TYR A 175 PHE 0.032 0.002 PHE D 331 TRP 0.023 0.002 TRP D 129 HIS 0.009 0.002 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00626 (24837) covalent geometry : angle 0.77862 (33672) SS BOND : bond 0.00636 ( 1) SS BOND : angle 4.06147 ( 2) hydrogen bonds : bond 0.04554 ( 1167) hydrogen bonds : angle 4.87338 ( 3384) metal coordination : bond 0.01694 ( 28) metal coordination : angle 7.76595 ( 45) link_TRANS : bond 0.00195 ( 7) link_TRANS : angle 0.68627 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 353 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8195 (ttmm) REVERT: A 167 LYS cc_start: 0.8586 (mttt) cc_final: 0.8369 (mttm) REVERT: A 425 ARG cc_start: 0.7216 (ttt180) cc_final: 0.6186 (tmt170) REVERT: A 529 LYS cc_start: 0.8283 (tttt) cc_final: 0.8023 (mttm) REVERT: A 621 ASN cc_start: 0.7545 (m110) cc_final: 0.7144 (t0) REVERT: A 650 MET cc_start: 0.5894 (mtp) cc_final: 0.5390 (ttm) REVERT: A 677 GLN cc_start: 0.8030 (mt0) cc_final: 0.7810 (mp10) REVERT: B 274 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7834 (tptp) REVERT: B 338 GLU cc_start: 0.6735 (mm-30) cc_final: 0.6221 (mm-30) REVERT: B 597 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8567 (pt) REVERT: B 751 LYS cc_start: 0.7357 (mttt) cc_final: 0.7037 (mmtt) REVERT: C 313 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6668 (mmt) REVERT: C 346 GLN cc_start: 0.5091 (mt0) cc_final: 0.4466 (pm20) REVERT: C 405 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: C 473 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7653 (ttp-110) REVERT: D 115 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6822 (ttm170) REVERT: D 247 LYS cc_start: 0.6677 (mttt) cc_final: 0.6155 (ptmm) REVERT: D 268 PHE cc_start: 0.8265 (m-10) cc_final: 0.7956 (m-80) REVERT: D 398 ARG cc_start: 0.6856 (tpt170) cc_final: 0.6523 (tpp-160) REVERT: D 433 PHE cc_start: 0.6249 (t80) cc_final: 0.6001 (t80) REVERT: E 249 LEU cc_start: 0.8637 (tp) cc_final: 0.8297 (mp) REVERT: E 308 CYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8343 (m) REVERT: E 331 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6655 (m-10) REVERT: F 150 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7647 (mt-10) REVERT: F 213 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7552 (tt) REVERT: G 5 LEU cc_start: 0.4660 (OUTLIER) cc_final: 0.4442 (tt) REVERT: H 71 GLU cc_start: 0.8195 (tt0) cc_final: 0.7296 (tm-30) REVERT: H 108 ASN cc_start: 0.7789 (m-40) cc_final: 0.7309 (m110) REVERT: H 155 ARG cc_start: 0.7615 (mtt180) cc_final: 0.6753 (ttp80) outliers start: 88 outliers final: 66 residues processed: 424 average time/residue: 0.1609 time to fit residues: 107.6491 Evaluate side-chains 412 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 336 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 308 CYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 144 GLN Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 186 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 150 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 162 optimal weight: 0.3980 chunk 7 optimal weight: 0.0470 chunk 179 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 71 optimal weight: 0.0870 chunk 209 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 262 optimal weight: 0.1980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.150076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.124153 restraints weight = 44774.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.126579 restraints weight = 27624.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127434 restraints weight = 19413.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128038 restraints weight = 18060.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128081 restraints weight = 15863.795| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24873 Z= 0.123 Angle : 0.711 21.304 33740 Z= 0.338 Chirality : 0.042 0.301 3863 Planarity : 0.004 0.066 4347 Dihedral : 5.152 53.029 3427 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.52 % Favored : 93.45 % Rotamer: Outliers : 2.45 % Allowed : 19.94 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.16), residues: 2870 helix: 1.04 (0.14), residues: 1426 sheet: -1.68 (0.28), residues: 332 loop : -2.41 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 345 TYR 0.023 0.001 TYR A 534 PHE 0.029 0.002 PHE D 331 TRP 0.023 0.001 TRP A 493 HIS 0.012 0.001 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00267 (24837) covalent geometry : angle 0.67256 (33672) SS BOND : bond 0.00623 ( 1) SS BOND : angle 3.81606 ( 2) hydrogen bonds : bond 0.03662 ( 1167) hydrogen bonds : angle 4.44676 ( 3384) metal coordination : bond 0.01118 ( 28) metal coordination : angle 6.26746 ( 45) link_TRANS : bond 0.00226 ( 7) link_TRANS : angle 0.58710 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5740 Ramachandran restraints generated. 2870 Oldfield, 0 Emsley, 2870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 388 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 157 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8526 (mttt) cc_final: 0.8262 (mttm) REVERT: A 425 ARG cc_start: 0.6966 (ttt180) cc_final: 0.6099 (tmt170) REVERT: A 511 TRP cc_start: 0.6493 (m-10) cc_final: 0.6198 (m-90) REVERT: A 522 TYR cc_start: 0.7911 (t80) cc_final: 0.7657 (t80) REVERT: A 529 LYS cc_start: 0.8212 (tttt) cc_final: 0.7892 (mttp) REVERT: A 571 TYR cc_start: 0.4476 (m-80) cc_final: 0.4223 (m-10) REVERT: A 621 ASN cc_start: 0.7457 (m110) cc_final: 0.7180 (t0) REVERT: A 650 MET cc_start: 0.5830 (mtp) cc_final: 0.5472 (ttm) REVERT: A 677 GLN cc_start: 0.7894 (mt0) cc_final: 0.7676 (mp10) REVERT: B 41 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: B 104 PHE cc_start: 0.7365 (t80) cc_final: 0.7010 (t80) REVERT: B 338 GLU cc_start: 0.6554 (mm-30) cc_final: 0.6331 (mm-30) REVERT: B 421 PHE cc_start: 0.7628 (p90) cc_final: 0.6898 (p90) REVERT: B 527 MET cc_start: 0.8494 (tpp) cc_final: 0.8087 (tpp) REVERT: B 543 GLN cc_start: 0.7093 (tp40) cc_final: 0.6856 (tm-30) REVERT: B 629 GLN cc_start: 0.5833 (tp-100) cc_final: 0.5290 (tt0) REVERT: C 226 GLN cc_start: 0.7121 (pt0) cc_final: 0.6519 (pt0) REVERT: C 313 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6661 (mmt) REVERT: C 346 GLN cc_start: 0.5007 (mt0) cc_final: 0.4469 (pm20) REVERT: C 528 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6458 (mtt) REVERT: C 534 ASN cc_start: 0.8096 (t0) cc_final: 0.7788 (m-40) REVERT: D 37 HIS cc_start: 0.6802 (OUTLIER) cc_final: 0.6282 (t-90) REVERT: D 57 MET cc_start: 0.8609 (mmm) cc_final: 0.8222 (mmm) REVERT: D 100 LEU cc_start: 0.6454 (tp) cc_final: 0.6218 (tp) REVERT: D 115 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7181 (ttm170) REVERT: D 247 LYS cc_start: 0.6610 (mttt) cc_final: 0.6153 (ptmm) REVERT: D 398 ARG cc_start: 0.6287 (tpt170) cc_final: 0.6044 (tpp-160) REVERT: E 308 CYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8369 (m) REVERT: E 331 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6721 (m-10) REVERT: F 213 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7228 (tt) REVERT: H 155 ARG cc_start: 0.7396 (mtt180) cc_final: 0.6784 (ttp80) outliers start: 61 outliers final: 44 residues processed: 432 average time/residue: 0.1616 time to fit residues: 109.3678 Evaluate side-chains 406 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 354 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain C residue 212 PRO Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 405 GLN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 308 CYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 276 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 30.0000 chunk 128 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 150 optimal weight: 0.4980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 36 GLN ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.146942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120966 restraints weight = 45152.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.122568 restraints weight = 29135.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123314 restraints weight = 20835.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.123909 restraints weight = 19923.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.124027 restraints weight = 17484.294| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24873 Z= 0.162 Angle : 0.753 22.614 33740 Z= 0.350 Chirality : 0.044 0.265 3863 Planarity : 0.004 0.073 4347 Dihedral : 5.216 54.627 3427 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.77 % Favored : 92.20 % Rotamer: Outliers : 2.53 % Allowed : 20.14 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.14 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.16), residues: 2870 helix: 1.03 (0.14), residues: 1425 sheet: -1.72 (0.29), residues: 334 loop : -2.37 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 345 TYR 0.027 0.002 TYR B 627 PHE 0.032 0.002 PHE D 331 TRP 0.023 0.002 TRP A 493 HIS 0.012 0.001 HIS D 264 Details of bonding type rmsd covalent geometry : bond 0.00376 (24837) covalent geometry : angle 0.69154 (33672) SS BOND : bond 0.00938 ( 1) SS BOND : angle 4.20932 ( 2) hydrogen bonds : bond 0.03839 ( 1167) hydrogen bonds : angle 4.58571 ( 3384) metal coordination : bond 0.01918 ( 28) metal coordination : angle 8.15322 ( 45) link_TRANS : bond 0.00182 ( 7) link_TRANS : angle 0.63520 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4199.73 seconds wall clock time: 73 minutes 15.75 seconds (4395.75 seconds total)