Starting phenix.real_space_refine on Mon Aug 10 05:08:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wn8_66110/08_2026/9wn8_66110_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wn8_66110/08_2026/9wn8_66110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wn8_66110/08_2026/9wn8_66110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wn8_66110/08_2026/9wn8_66110.map" model { file = "/net/cci-nas-00/data/ceres_data/9wn8_66110/08_2026/9wn8_66110_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wn8_66110/08_2026/9wn8_66110_neut.cif" } resolution = 2.81 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= -0.001 sd= 0.039 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: 5 Type Number sf(0) Gaussians P 412 5.49 5 S 72 5.16 5 C 25476 2.51 5 N 7092 2.21 5 O 8890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 192 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41942 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2867 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 10, 'TRANS': 343} Chain breaks: 1 Chain: "B" Number of atoms: 5479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5479 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 18, 'TRANS': 645} Chain breaks: 6 Chain: "C" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1346 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 23} Link IDs: {'rna2p': 7, 'rna3p': 55} Chain breaks: 1 Chain: "D" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 819 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 2 Chain: "E" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2867 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 10, 'TRANS': 343} Chain breaks: 1 Chain: "F" Number of atoms: 5437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5437 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 18, 'TRANS': 641} Chain breaks: 6 Chain: "G" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1346 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 32, 'rna3p_pyr': 23} Link IDs: {'rna2p': 8, 'rna3p': 54} Chain breaks: 1 Chain: "H" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 819 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 2 Chain: "I" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2867 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 10, 'TRANS': 343} Chain breaks: 1 Chain: "J" Number of atoms: 5419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5419 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 18, 'TRANS': 639} Chain breaks: 6 Chain: "K" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1346 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 24} Link IDs: {'rna2p': 7, 'rna3p': 55} Chain breaks: 1 Chain: "L" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 819 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 2 Chain: "M" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2867 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 10, 'TRANS': 343} Chain breaks: 1 Chain: "N" Number of atoms: 5479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5479 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 18, 'TRANS': 645} Chain breaks: 6 Chain: "O" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1346 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 32, 'rna3p_pyr': 23} Link IDs: {'rna2p': 8, 'rna3p': 54} Chain breaks: 1 Chain: "P" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 819 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 2 Time building chain proxies: 7.76, per 1000 atoms: 0.19 Number of scatterers: 41942 At special positions: 0 Unit cell: (110.818, 185.248, 234.041, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 412 15.00 O 8890 8.00 N 7092 7.00 C 25476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7812 Finding SS restraints... Secondary structure from input PDB file: 209 helices and 33 sheets defined 58.6% alpha, 10.6% beta 88 base pairs and 144 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.569A pdb=" N LEU A 18 " --> pdb=" O TYR A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 29 removed outlier: 3.520A pdb=" N ILE A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 60 through 71 Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.626A pdb=" N TYR A 99 " --> pdb=" O PRO A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.696A pdb=" N SER A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.685A pdb=" N ILE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 283 Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.671A pdb=" N ILE A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 344 removed outlier: 3.739A pdb=" N LEU A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 371 removed outlier: 3.923A pdb=" N ASN A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 51 Processing helix chain 'B' and resid 76 through 85 removed outlier: 3.555A pdb=" N SER B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 100 Processing helix chain 'B' and resid 101 through 107 removed outlier: 3.950A pdb=" N LYS B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 143 through 154 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 169 through 179 Processing helix chain 'B' and resid 188 through 201 removed outlier: 3.693A pdb=" N LYS B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 224 through 237 Processing helix chain 'B' and resid 257 through 274 Processing helix chain 'B' and resid 292 through 311 removed outlier: 3.515A pdb=" N PHE B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 347 removed outlier: 3.515A pdb=" N LEU B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 380 Processing helix chain 'B' and resid 382 through 389 removed outlier: 4.038A pdb=" N PHE B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 408 through 414 removed outlier: 3.698A pdb=" N LEU B 414 " --> pdb=" O SER B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 removed outlier: 3.600A pdb=" N LEU B 420 " --> pdb=" O PRO B 416 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 435 Processing helix chain 'B' and resid 436 through 440 removed outlier: 4.191A pdb=" N LYS B 440 " --> pdb=" O GLY B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 487 through 504 Processing helix chain 'B' and resid 521 through 532 Processing helix chain 'B' and resid 542 through 548 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.829A pdb=" N THR B 566 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 636 removed outlier: 4.563A pdb=" N PHE B 636 " --> pdb=" O VAL B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 removed outlier: 4.042A pdb=" N ILE B 642 " --> pdb=" O ASN B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 667 Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 696 through 713 Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 729 through 749 removed outlier: 4.443A pdb=" N SER B 746 " --> pdb=" O GLU B 742 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER B 747 " --> pdb=" O ALA B 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 18 Processing helix chain 'E' and resid 23 through 29 removed outlier: 3.930A pdb=" N ILE E 27 " --> pdb=" O PHE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 71 Processing helix chain 'E' and resid 72 through 75 Processing helix chain 'E' and resid 89 through 95 Processing helix chain 'E' and resid 96 through 100 removed outlier: 3.697A pdb=" N TYR E 99 " --> pdb=" O PRO E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 115 Processing helix chain 'E' and resid 116 through 125 removed outlier: 3.527A pdb=" N VAL E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 149 removed outlier: 3.676A pdb=" N SER E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL E 148 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 Processing helix chain 'E' and resid 177 through 190 Processing helix chain 'E' and resid 215 through 227 removed outlier: 3.586A pdb=" N ILE E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 282 Processing helix chain 'E' and resid 286 through 294 removed outlier: 3.597A pdb=" N ILE E 290 " --> pdb=" O PRO E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 344 removed outlier: 3.582A pdb=" N LEU E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 371 Processing helix chain 'F' and resid 32 through 51 Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 90 through 100 Processing helix chain 'F' and resid 101 through 107 removed outlier: 4.146A pdb=" N LYS F 107 " --> pdb=" O SER F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 118 Processing helix chain 'F' and resid 143 through 154 Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 169 through 179 Processing helix chain 'F' and resid 188 through 201 removed outlier: 3.601A pdb=" N LYS F 199 " --> pdb=" O PHE F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 219 Processing helix chain 'F' and resid 224 through 237 Processing helix chain 'F' and resid 257 through 274 removed outlier: 3.527A pdb=" N ARG F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 311 Processing helix chain 'F' and resid 335 through 347 removed outlier: 3.599A pdb=" N LEU F 339 " --> pdb=" O SER F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 380 Processing helix chain 'F' and resid 382 through 388 Processing helix chain 'F' and resid 399 through 407 Processing helix chain 'F' and resid 408 through 415 removed outlier: 3.841A pdb=" N LEU F 414 " --> pdb=" O SER F 410 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR F 415 " --> pdb=" O LEU F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.696A pdb=" N LEU F 420 " --> pdb=" O PRO F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 435 Processing helix chain 'F' and resid 436 through 440 removed outlier: 3.936A pdb=" N LYS F 440 " --> pdb=" O GLY F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 454 No H-bonds generated for 'chain 'F' and resid 452 through 454' Processing helix chain 'F' and resid 467 through 477 Processing helix chain 'F' and resid 487 through 504 Processing helix chain 'F' and resid 509 through 513 Processing helix chain 'F' and resid 521 through 532 Processing helix chain 'F' and resid 542 through 548 Processing helix chain 'F' and resid 551 through 566 removed outlier: 4.282A pdb=" N TYR F 555 " --> pdb=" O GLN F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 636 removed outlier: 4.036A pdb=" N PHE F 636 " --> pdb=" O VAL F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 650 removed outlier: 4.294A pdb=" N ILE F 642 " --> pdb=" O ASN F 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 666 removed outlier: 3.936A pdb=" N ASP F 666 " --> pdb=" O LYS F 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 669 through 681 Processing helix chain 'F' and resid 692 through 695 Processing helix chain 'F' and resid 696 through 713 Processing helix chain 'F' and resid 715 through 724 removed outlier: 4.001A pdb=" N ILE F 719 " --> pdb=" O ASP F 715 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG F 720 " --> pdb=" O ASP F 716 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 749 removed outlier: 3.559A pdb=" N SER F 747 " --> pdb=" O ALA F 743 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 18 Processing helix chain 'I' and resid 23 through 29 Processing helix chain 'I' and resid 58 through 71 removed outlier: 3.544A pdb=" N HIS I 62 " --> pdb=" O SER I 58 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL I 63 " --> pdb=" O PRO I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 75 Processing helix chain 'I' and resid 89 through 95 Processing helix chain 'I' and resid 96 through 100 removed outlier: 3.695A pdb=" N TYR I 99 " --> pdb=" O PRO I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 115 Processing helix chain 'I' and resid 116 through 125 Processing helix chain 'I' and resid 126 through 128 No H-bonds generated for 'chain 'I' and resid 126 through 128' Processing helix chain 'I' and resid 140 through 149 removed outlier: 3.681A pdb=" N VAL I 148 " --> pdb=" O ILE I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 177 Processing helix chain 'I' and resid 177 through 191 Processing helix chain 'I' and resid 215 through 227 removed outlier: 3.748A pdb=" N ILE I 219 " --> pdb=" O SER I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 283 Processing helix chain 'I' and resid 286 through 294 Processing helix chain 'I' and resid 310 through 344 removed outlier: 3.688A pdb=" N LEU I 336 " --> pdb=" O TYR I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 370 Processing helix chain 'J' and resid 32 through 51 Processing helix chain 'J' and resid 76 through 85 removed outlier: 3.627A pdb=" N SER J 85 " --> pdb=" O LYS J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 101 Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.782A pdb=" N LYS J 107 " --> pdb=" O SER J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 Processing helix chain 'J' and resid 143 through 154 Processing helix chain 'J' and resid 162 through 164 No H-bonds generated for 'chain 'J' and resid 162 through 164' Processing helix chain 'J' and resid 169 through 179 Processing helix chain 'J' and resid 188 through 201 removed outlier: 3.528A pdb=" N LYS J 199 " --> pdb=" O PHE J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 219 Processing helix chain 'J' and resid 224 through 237 Processing helix chain 'J' and resid 257 through 274 Processing helix chain 'J' and resid 292 through 311 removed outlier: 3.661A pdb=" N PHE J 310 " --> pdb=" O ILE J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 347 removed outlier: 3.546A pdb=" N LEU J 339 " --> pdb=" O SER J 335 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY J 347 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 380 Processing helix chain 'J' and resid 382 through 388 removed outlier: 3.526A pdb=" N LEU J 388 " --> pdb=" O ASN J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 389 through 391 No H-bonds generated for 'chain 'J' and resid 389 through 391' Processing helix chain 'J' and resid 399 through 407 removed outlier: 3.703A pdb=" N LEU J 403 " --> pdb=" O GLY J 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 414 removed outlier: 4.226A pdb=" N LEU J 414 " --> pdb=" O SER J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 415 through 421 removed outlier: 3.566A pdb=" N SER J 419 " --> pdb=" O TYR J 415 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU J 420 " --> pdb=" O PRO J 416 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA J 421 " --> pdb=" O ALA J 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 415 through 421' Processing helix chain 'J' and resid 427 through 435 Processing helix chain 'J' and resid 436 through 440 removed outlier: 3.665A pdb=" N LYS J 440 " --> pdb=" O GLY J 437 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 454 No H-bonds generated for 'chain 'J' and resid 452 through 454' Processing helix chain 'J' and resid 467 through 476 Processing helix chain 'J' and resid 487 through 503 Processing helix chain 'J' and resid 523 through 532 Processing helix chain 'J' and resid 542 through 548 Processing helix chain 'J' and resid 552 through 566 removed outlier: 3.970A pdb=" N THR J 566 " --> pdb=" O ASP J 562 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 636 removed outlier: 4.647A pdb=" N PHE J 636 " --> pdb=" O VAL J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 649 removed outlier: 4.100A pdb=" N ILE J 642 " --> pdb=" O ASN J 638 " (cutoff:3.500A) Processing helix chain 'J' and resid 659 through 667 removed outlier: 3.864A pdb=" N ASP J 666 " --> pdb=" O LYS J 662 " (cutoff:3.500A) Processing helix chain 'J' and resid 669 through 684 removed outlier: 3.697A pdb=" N ARG J 673 " --> pdb=" O ALA J 669 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN J 682 " --> pdb=" O ASN J 678 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU J 683 " --> pdb=" O TYR J 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 696 through 713 Processing helix chain 'J' and resid 715 through 724 removed outlier: 3.948A pdb=" N ILE J 719 " --> pdb=" O ASP J 715 " (cutoff:3.500A) Processing helix chain 'J' and resid 729 through 749 removed outlier: 4.155A pdb=" N SER J 746 " --> pdb=" O GLU J 742 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER J 747 " --> pdb=" O ALA J 743 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 17 Processing helix chain 'M' and resid 23 through 29 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 58 through 71 removed outlier: 3.989A pdb=" N HIS M 62 " --> pdb=" O SER M 58 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL M 63 " --> pdb=" O PRO M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 75 removed outlier: 3.697A pdb=" N ILE M 75 " --> pdb=" O LEU M 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 72 through 75' Processing helix chain 'M' and resid 89 through 95 Processing helix chain 'M' and resid 96 through 100 removed outlier: 3.784A pdb=" N TYR M 99 " --> pdb=" O PRO M 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 115 Processing helix chain 'M' and resid 116 through 125 Processing helix chain 'M' and resid 126 through 128 No H-bonds generated for 'chain 'M' and resid 126 through 128' Processing helix chain 'M' and resid 140 through 149 removed outlier: 3.688A pdb=" N SER M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL M 148 " --> pdb=" O ILE M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 158 Processing helix chain 'M' and resid 168 through 177 Processing helix chain 'M' and resid 177 through 191 Processing helix chain 'M' and resid 215 through 227 removed outlier: 3.690A pdb=" N ILE M 219 " --> pdb=" O SER M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 283 Processing helix chain 'M' and resid 286 through 295 removed outlier: 3.615A pdb=" N ILE M 295 " --> pdb=" O CYS M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 344 removed outlier: 3.668A pdb=" N LEU M 336 " --> pdb=" O TYR M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 370 Processing helix chain 'N' and resid 32 through 51 Processing helix chain 'N' and resid 76 through 85 removed outlier: 3.581A pdb=" N SER N 85 " --> pdb=" O LYS N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 100 Processing helix chain 'N' and resid 101 through 107 removed outlier: 4.295A pdb=" N LYS N 107 " --> pdb=" O SER N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 118 Processing helix chain 'N' and resid 143 through 154 removed outlier: 3.538A pdb=" N ARG N 147 " --> pdb=" O ASP N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 169 through 179 Processing helix chain 'N' and resid 188 through 201 removed outlier: 3.724A pdb=" N LYS N 199 " --> pdb=" O PHE N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 219 Processing helix chain 'N' and resid 224 through 237 Processing helix chain 'N' and resid 257 through 274 Processing helix chain 'N' and resid 292 through 311 removed outlier: 3.583A pdb=" N PHE N 310 " --> pdb=" O ILE N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 347 removed outlier: 3.563A pdb=" N LEU N 339 " --> pdb=" O SER N 335 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 380 Processing helix chain 'N' and resid 382 through 387 Processing helix chain 'N' and resid 399 through 407 removed outlier: 3.562A pdb=" N LEU N 403 " --> pdb=" O GLY N 399 " (cutoff:3.500A) Processing helix chain 'N' and resid 408 through 414 removed outlier: 3.695A pdb=" N LEU N 414 " --> pdb=" O SER N 410 " (cutoff:3.500A) Processing helix chain 'N' and resid 415 through 421 removed outlier: 3.516A pdb=" N SER N 419 " --> pdb=" O TYR N 415 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU N 420 " --> pdb=" O PRO N 416 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA N 421 " --> pdb=" O ALA N 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 415 through 421' Processing helix chain 'N' and resid 427 through 435 Processing helix chain 'N' and resid 436 through 440 removed outlier: 3.723A pdb=" N LYS N 440 " --> pdb=" O GLY N 437 " (cutoff:3.500A) Processing helix chain 'N' and resid 452 through 454 No H-bonds generated for 'chain 'N' and resid 452 through 454' Processing helix chain 'N' and resid 467 through 477 Processing helix chain 'N' and resid 487 through 504 Processing helix chain 'N' and resid 521 through 532 Processing helix chain 'N' and resid 542 through 548 Processing helix chain 'N' and resid 552 through 566 Processing helix chain 'N' and resid 619 through 636 removed outlier: 4.058A pdb=" N PHE N 636 " --> pdb=" O VAL N 632 " (cutoff:3.500A) Processing helix chain 'N' and resid 638 through 650 removed outlier: 3.801A pdb=" N ILE N 642 " --> pdb=" O ASN N 638 " (cutoff:3.500A) Processing helix chain 'N' and resid 659 through 667 Processing helix chain 'N' and resid 669 through 682 removed outlier: 3.809A pdb=" N ASN N 682 " --> pdb=" O ASN N 678 " (cutoff:3.500A) Processing helix chain 'N' and resid 692 through 695 Processing helix chain 'N' and resid 696 through 713 Processing helix chain 'N' and resid 715 through 724 Processing helix chain 'N' and resid 729 through 749 removed outlier: 4.465A pdb=" N SER N 746 " --> pdb=" O GLU N 742 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER N 747 " --> pdb=" O ALA N 743 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 198 Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 removed outlier: 3.831A pdb=" N ILE A 134 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 19 removed outlier: 7.134A pdb=" N ASP B 15 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE B 3 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASP B 75 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU B 11 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 11.299A pdb=" N VAL B 67 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 156 through 160 removed outlier: 5.969A pdb=" N VAL B 282 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER B 332 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE B 284 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 25 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU B 353 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N CYS B 27 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N PHE B 355 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 29 " --> pdb=" O PHE B 355 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N LYS B 357 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL B 352 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 422 through 425 removed outlier: 5.950A pdb=" N VAL B 395 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 394 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE B 448 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE B 396 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASP B 450 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N TYR B 537 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE B 447 " --> pdb=" O TYR B 537 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET B 539 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS B 449 " --> pdb=" O MET B 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AB1, first strand: chain 'E' and resid 41 through 44 Processing sheet with id=AB2, first strand: chain 'E' and resid 194 through 198 Processing sheet with id=AB3, first strand: chain 'E' and resid 132 through 134 removed outlier: 3.520A pdb=" N ILE E 134 " --> pdb=" O GLN E 138 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 244 through 247 Processing sheet with id=AB5, first strand: chain 'F' and resid 14 through 19 removed outlier: 7.203A pdb=" N ASP F 15 " --> pdb=" O ASN F 10 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE F 3 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASP F 75 " --> pdb=" O ILE F 3 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU F 11 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N VAL F 67 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 156 through 160 removed outlier: 6.563A pdb=" N LEU F 157 " --> pdb=" O TYR F 283 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASP F 285 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE F 159 " --> pdb=" O ASP F 285 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL F 282 " --> pdb=" O PHE F 330 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N SER F 332 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE F 284 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE F 25 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU F 353 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N CYS F 27 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE F 355 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE F 29 " --> pdb=" O PHE F 355 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N LYS F 357 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 422 through 425 removed outlier: 6.289A pdb=" N ILE F 394 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE F 448 " --> pdb=" O ILE F 394 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE F 396 " --> pdb=" O ILE F 448 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ASP F 450 " --> pdb=" O PHE F 396 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 41 through 44 Processing sheet with id=AB9, first strand: chain 'I' and resid 194 through 198 Processing sheet with id=AC1, first strand: chain 'I' and resid 132 through 134 removed outlier: 6.956A pdb=" N GLN I 138 " --> pdb=" O LEU I 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 150 through 151 Processing sheet with id=AC3, first strand: chain 'I' and resid 244 through 247 Processing sheet with id=AC4, first strand: chain 'J' and resid 14 through 20 removed outlier: 7.250A pdb=" N ASP J 15 " --> pdb=" O ASN J 10 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE J 3 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ASP J 75 " --> pdb=" O ILE J 3 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU J 11 " --> pdb=" O VAL J 67 " (cutoff:3.500A) removed outlier: 11.481A pdb=" N VAL J 67 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 156 through 160 removed outlier: 5.977A pdb=" N VAL J 282 " --> pdb=" O PHE J 330 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER J 332 " --> pdb=" O VAL J 282 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE J 284 " --> pdb=" O SER J 332 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL J 352 " --> pdb=" O ILE J 368 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 422 through 425 removed outlier: 6.034A pdb=" N VAL J 395 " --> pdb=" O TYR J 424 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE J 394 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE J 448 " --> pdb=" O ILE J 394 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE J 396 " --> pdb=" O ILE J 448 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASP J 450 " --> pdb=" O PHE J 396 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 41 through 44 Processing sheet with id=AC8, first strand: chain 'M' and resid 194 through 198 Processing sheet with id=AC9, first strand: chain 'M' and resid 132 through 134 removed outlier: 3.872A pdb=" N GLN M 138 " --> pdb=" O ILE M 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 150 through 151 Processing sheet with id=AD2, first strand: chain 'M' and resid 244 through 247 Processing sheet with id=AD3, first strand: chain 'N' and resid 14 through 19 removed outlier: 6.948A pdb=" N ASP N 15 " --> pdb=" O ASN N 10 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR N 73 " --> pdb=" O GLU N 4 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE N 6 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR N 71 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL N 8 " --> pdb=" O GLU N 69 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU N 69 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN N 10 " --> pdb=" O VAL N 67 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL N 67 " --> pdb=" O ASN N 10 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 156 through 160 removed outlier: 6.037A pdb=" N VAL N 282 " --> pdb=" O PHE N 330 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N SER N 332 " --> pdb=" O VAL N 282 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE N 284 " --> pdb=" O SER N 332 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL N 352 " --> pdb=" O ILE N 368 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 422 through 425 removed outlier: 5.887A pdb=" N VAL N 395 " --> pdb=" O TYR N 424 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 508 through 509 1735 hydrogen bonds defined for protein. 5055 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 223 hydrogen bonds 428 hydrogen bond angles 0 basepair planarities 88 basepair parallelities 144 stacking parallelities Total time for adding SS restraints: 8.05 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5956 1.31 - 1.44: 13988 1.44 - 1.56: 22741 1.56 - 1.69: 808 1.69 - 1.82: 120 Bond restraints: 43613 Sorted by residual: bond pdb=" C6 G G 34 " pdb=" N1 G G 34 " ideal model delta sigma weight residual 1.391 1.354 0.037 7.00e-03 2.04e+04 2.73e+01 bond pdb=" C1' DT D 72 " pdb=" N1 DT D 72 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" C1' DT D 73 " pdb=" N1 DT D 73 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.11e+01 bond pdb=" C2 DT D 72 " pdb=" O2 DT D 72 " ideal model delta sigma weight residual 1.220 1.185 0.035 8.00e-03 1.56e+04 1.97e+01 bond pdb=" C6 A C 47 " pdb=" N1 A C 47 " ideal model delta sigma weight residual 1.351 1.320 0.031 7.00e-03 2.04e+04 1.92e+01 ... (remaining 43608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 59860 2.96 - 5.93: 704 5.93 - 8.89: 82 8.89 - 11.85: 13 11.85 - 14.82: 5 Bond angle restraints: 60664 Sorted by residual: angle pdb=" O4 U G 41 " pdb=" C4 U G 41 " pdb=" C5 U G 41 " ideal model delta sigma weight residual 125.90 136.82 -10.92 6.00e-01 2.78e+00 3.31e+02 angle pdb=" O4 U C 61 " pdb=" C4 U C 61 " pdb=" C5 U C 61 " ideal model delta sigma weight residual 125.90 136.67 -10.77 6.00e-01 2.78e+00 3.22e+02 angle pdb=" N3 U C 61 " pdb=" C4 U C 61 " pdb=" O4 U C 61 " ideal model delta sigma weight residual 119.40 106.87 12.53 7.00e-01 2.04e+00 3.21e+02 angle pdb=" N3 U G 41 " pdb=" C4 U G 41 " pdb=" O4 U G 41 " ideal model delta sigma weight residual 119.40 107.19 12.21 7.00e-01 2.04e+00 3.04e+02 angle pdb=" N3 C G 40 " pdb=" C4 C G 40 " pdb=" N4 C G 40 " ideal model delta sigma weight residual 118.00 105.81 12.19 7.00e-01 2.04e+00 3.03e+02 ... (remaining 60659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 23896 34.44 - 68.89: 2157 68.89 - 103.33: 136 103.33 - 137.77: 13 137.77 - 172.22: 18 Dihedral angle restraints: 26220 sinusoidal: 14174 harmonic: 12046 Sorted by residual: dihedral pdb=" C4' C O 56 " pdb=" C3' C O 56 " pdb=" C2' C O 56 " pdb=" C1' C O 56 " ideal model delta sinusoidal sigma weight residual -35.00 33.18 -68.18 1 8.00e+00 1.56e-02 9.42e+01 dihedral pdb=" C4' C C 56 " pdb=" C3' C C 56 " pdb=" C2' C C 56 " pdb=" C1' C C 56 " ideal model delta sinusoidal sigma weight residual -35.00 32.84 -67.84 1 8.00e+00 1.56e-02 9.34e+01 dihedral pdb=" C4' G O 18 " pdb=" C3' G O 18 " pdb=" C2' G O 18 " pdb=" C1' G O 18 " ideal model delta sinusoidal sigma weight residual -35.00 29.93 -64.93 1 8.00e+00 1.56e-02 8.65e+01 ... (remaining 26217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 6113 0.084 - 0.168: 891 0.168 - 0.251: 32 0.251 - 0.335: 2 0.335 - 0.419: 3 Chirality restraints: 7041 Sorted by residual: chirality pdb=" CG LEU F 663 " pdb=" CB LEU F 663 " pdb=" CD1 LEU F 663 " pdb=" CD2 LEU F 663 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" C1' A G 17 " pdb=" O4' A G 17 " pdb=" C2' A G 17 " pdb=" N9 A G 17 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C1' A G 19 " pdb=" O4' A G 19 " pdb=" C2' A G 19 " pdb=" N9 A G 19 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 7038 not shown) Planarity restraints: 6119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U G 61 " 0.015 2.00e-02 2.50e+03 2.58e-02 1.50e+01 pdb=" N1 U G 61 " -0.010 2.00e-02 2.50e+03 pdb=" C2 U G 61 " 0.014 2.00e-02 2.50e+03 pdb=" O2 U G 61 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U G 61 " -0.010 2.00e-02 2.50e+03 pdb=" C4 U G 61 " -0.056 2.00e-02 2.50e+03 pdb=" O4 U G 61 " 0.046 2.00e-02 2.50e+03 pdb=" C5 U G 61 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U G 61 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT D 71 " 0.045 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" N1 DT D 71 " -0.055 2.00e-02 2.50e+03 pdb=" C2 DT D 71 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT D 71 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DT D 71 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DT D 71 " 0.010 2.00e-02 2.50e+03 pdb=" O4 DT D 71 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT D 71 " 0.005 2.00e-02 2.50e+03 pdb=" C7 DT D 71 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT D 71 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 61 " -0.008 2.00e-02 2.50e+03 2.08e-02 9.74e+00 pdb=" N1 U C 61 " 0.006 2.00e-02 2.50e+03 pdb=" C2 U C 61 " -0.020 2.00e-02 2.50e+03 pdb=" O2 U C 61 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U C 61 " 0.032 2.00e-02 2.50e+03 pdb=" C4 U C 61 " 0.031 2.00e-02 2.50e+03 pdb=" O4 U C 61 " -0.037 2.00e-02 2.50e+03 pdb=" C5 U C 61 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U C 61 " -0.001 2.00e-02 2.50e+03 ... (remaining 6116 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6688 2.76 - 3.29: 39942 3.29 - 3.83: 73768 3.83 - 4.36: 86044 4.36 - 4.90: 139396 Nonbonded interactions: 345838 Sorted by model distance: nonbonded pdb=" O GLN B 657 " pdb=" OE1 GLN B 657 " model vdw 2.221 3.040 nonbonded pdb=" OG SER A 331 " pdb=" O4 DT D 71 " model vdw 2.349 3.040 nonbonded pdb=" N1 A G 25 " pdb=" O4 U G 68 " model vdw 2.362 2.496 nonbonded pdb=" O THR B 699 " pdb=" OD1 ASN B 703 " model vdw 2.378 3.040 nonbonded pdb=" O3' DT D 71 " pdb=" O2 DT D 72 " model vdw 2.380 3.040 ... (remaining 345833 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = (chain 'B' and (resid 2 through 514 or resid 522 through 749)) selection = (chain 'F' and (resid 2 through 514 or resid 522 through 749)) selection = chain 'J' selection = (chain 'N' and (resid 2 through 514 or resid 522 through 749)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 36.840 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.090 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:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 43613 Z= 0.373 Angle : 0.887 14.815 60664 Z= 0.652 Chirality : 0.055 0.419 7041 Planarity : 0.005 0.065 6119 Dihedral : 22.489 172.217 18408 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.35 % Allowed : 31.56 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 3990 helix: 0.74 (0.11), residues: 2056 sheet: 0.15 (0.21), residues: 554 loop : -0.50 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 42 TYR 0.048 0.002 TYR B 704 PHE 0.022 0.002 PHE F 330 TRP 0.045 0.003 TRP F 697 HIS 0.020 0.002 HIS F 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.37 (43613) covalent geometry : angle 0.88718 / 0.65 (60664) hydrogen bonds : bond 0.13040 / 8.53 ( 1958) hydrogen bonds : angle 5.62896 / 4.01 ( 5483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 578 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7836 (ttmm) cc_final: 0.7549 (ttpp) REVERT: A 160 MET cc_start: 0.7062 (tpt) cc_final: 0.6590 (mtp) REVERT: A 211 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7254 (ptmt) REVERT: A 339 PHE cc_start: 0.7558 (t80) cc_final: 0.7263 (t80) REVERT: A 353 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: B 59 ASP cc_start: 0.8194 (m-30) cc_final: 0.7972 (m-30) REVERT: B 81 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7915 (mttt) REVERT: B 89 ASN cc_start: 0.6275 (m-40) cc_final: 0.5701 (p0) REVERT: B 119 SER cc_start: 0.8373 (t) cc_final: 0.8165 (p) REVERT: B 157 LEU cc_start: 0.7717 (mp) cc_final: 0.7368 (tt) REVERT: B 260 LYS cc_start: 0.7299 (tptt) cc_final: 0.7005 (ttpt) REVERT: B 307 TYR cc_start: 0.7521 (t80) cc_final: 0.7272 (t80) REVERT: B 359 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7446 (mppt) REVERT: B 398 GLU cc_start: 0.7688 (tp30) cc_final: 0.7271 (tp30) REVERT: B 440 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7837 (mttm) REVERT: B 553 LEU cc_start: 0.5823 (tp) cc_final: 0.5605 (mt) REVERT: B 641 GLU cc_start: 0.5115 (mt-10) cc_final: 0.4457 (mt-10) REVERT: B 690 GLN cc_start: 0.3890 (pm20) cc_final: 0.3463 (pm20) REVERT: B 736 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7423 (mm-40) REVERT: E 105 ARG cc_start: 0.7528 (ttt-90) cc_final: 0.7204 (ttt-90) REVERT: E 107 ASP cc_start: 0.7369 (m-30) cc_final: 0.6921 (t0) REVERT: F 82 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.7005 (mm) REVERT: F 183 ASN cc_start: 0.6589 (p0) cc_final: 0.6117 (t0) REVERT: F 198 GLU cc_start: 0.8101 (tt0) cc_final: 0.7886 (mm-30) REVERT: F 219 ASP cc_start: 0.7199 (m-30) cc_final: 0.6869 (m-30) REVERT: F 275 THR cc_start: 0.8558 (p) cc_final: 0.8354 (t) REVERT: F 375 GLU cc_start: 0.7133 (pp20) cc_final: 0.6568 (mp0) REVERT: F 429 VAL cc_start: 0.6305 (OUTLIER) cc_final: 0.5905 (t) REVERT: F 435 ASN cc_start: 0.7564 (t0) cc_final: 0.6965 (t0) REVERT: I 72 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7487 (mp) REVERT: I 141 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7893 (tp) REVERT: I 209 GLU cc_start: 0.7641 (tp30) cc_final: 0.7083 (mp0) REVERT: J 21 ASP cc_start: 0.7896 (m-30) cc_final: 0.7455 (m-30) REVERT: J 91 ARG cc_start: 0.5826 (tpt170) cc_final: 0.3686 (mtp180) REVERT: J 180 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7296 (p0) REVERT: J 197 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.5880 (t0) REVERT: J 294 LYS cc_start: 0.7212 (pttt) cc_final: 0.6636 (mmmm) REVERT: J 376 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.6173 (tmt170) REVERT: M 38 ASN cc_start: 0.8047 (t0) cc_final: 0.7464 (t0) REVERT: M 42 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7436 (ttp-110) REVERT: M 211 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7902 (mtpt) REVERT: M 253 GLU cc_start: 0.7380 (tp30) cc_final: 0.7074 (tm-30) REVERT: M 268 LYS cc_start: 0.7523 (mmmm) cc_final: 0.7237 (mmmt) REVERT: M 288 LYS cc_start: 0.6593 (tptp) cc_final: 0.6312 (mmtt) REVERT: M 329 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7671 (t80) REVERT: N 69 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7198 (tm-30) REVERT: N 86 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7187 (tpp-160) REVERT: N 174 LYS cc_start: 0.7651 (mtpp) cc_final: 0.7409 (ttpt) REVERT: N 260 LYS cc_start: 0.6755 (tmtt) cc_final: 0.6047 (tptp) REVERT: N 379 ASN cc_start: 0.8450 (m-40) cc_final: 0.8138 (m-40) REVERT: N 440 LYS cc_start: 0.8302 (ptpp) cc_final: 0.8095 (ptmt) REVERT: N 551 GLN cc_start: 0.6444 (OUTLIER) cc_final: 0.6186 (tm-30) REVERT: N 558 ASN cc_start: 0.6947 (m-40) cc_final: 0.6585 (m-40) outliers start: 89 outliers final: 29 residues processed: 642 average time/residue: 0.5420 time to fit residues: 444.6132 Evaluate side-chains 402 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 359 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain J residue 118 ASN Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 180 ASN Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain J residue 376 ARG Chi-restraints excluded: chain J residue 698 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 251 VAL Chi-restraints excluded: chain M residue 329 TYR Chi-restraints excluded: chain M residue 337 VAL Chi-restraints excluded: chain N residue 86 ARG Chi-restraints excluded: chain N residue 551 GLN Chi-restraints excluded: chain N residue 700 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 ASN A 30 GLN ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN B 433 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 ASN F 267 HIS ** F 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 ASN I 113 ASN I 138 GLN J 341 GLN ** J 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 GLN ** M 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN ** N 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.233710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.173641 restraints weight = 50819.184| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.65 r_work: 0.3806 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 43613 Z= 0.242 Angle : 0.699 9.567 60664 Z= 0.386 Chirality : 0.048 0.309 7041 Planarity : 0.005 0.054 6119 Dihedral : 23.032 178.172 10110 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 96.99 % Rotamer: Outliers : 6.60 % Allowed : 26.62 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 3990 helix: 0.73 (0.11), residues: 2063 sheet: -0.08 (0.21), residues: 552 loop : -0.45 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 69 TYR 0.029 0.002 TYR B 704 PHE 0.021 0.002 PHE N 277 TRP 0.017 0.002 TRP F 697 HIS 0.011 0.001 HIS F 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 (43613) covalent geometry : angle 0.69874 / 0.39 (60664) hydrogen bonds : bond 0.05318 / 3.47 ( 1958) hydrogen bonds : angle 4.79927 / 3.41 ( 5483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 375 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.4498 (mpp) cc_final: 0.4222 (mpt) REVERT: A 16 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7424 (ttpt) REVERT: A 62 HIS cc_start: 0.5006 (OUTLIER) cc_final: 0.4571 (m90) REVERT: A 142 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: A 160 MET cc_start: 0.7273 (tpt) cc_final: 0.6906 (mtp) REVERT: A 250 TYR cc_start: 0.8530 (m-80) cc_final: 0.8246 (m-80) REVERT: A 315 LYS cc_start: 0.5624 (OUTLIER) cc_final: 0.5087 (ptpt) REVERT: A 329 TYR cc_start: 0.4832 (t80) cc_final: 0.4487 (m-80) REVERT: A 339 PHE cc_start: 0.7665 (t80) cc_final: 0.7385 (t80) REVERT: A 353 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: B 3 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8073 (mp) REVERT: B 89 ASN cc_start: 0.6820 (m-40) cc_final: 0.5945 (p0) REVERT: B 157 LEU cc_start: 0.7779 (mp) cc_final: 0.7382 (tt) REVERT: B 260 LYS cc_start: 0.7525 (tptt) cc_final: 0.7298 (tptm) REVERT: B 286 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: B 359 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7528 (mptt) REVERT: B 414 LEU cc_start: 0.7323 (pt) cc_final: 0.6519 (mt) REVERT: B 473 MET cc_start: 0.1576 (OUTLIER) cc_final: 0.0576 (tmm) REVERT: B 501 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7447 (tp) REVERT: B 551 GLN cc_start: 0.6131 (mp10) cc_final: 0.5488 (pt0) REVERT: B 641 GLU cc_start: 0.5011 (mt-10) cc_final: 0.4667 (mm-30) REVERT: B 690 GLN cc_start: 0.3395 (pm20) cc_final: 0.2668 (tm-30) REVERT: B 736 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7272 (mm-40) REVERT: E 40 GLU cc_start: 0.5021 (OUTLIER) cc_final: 0.4770 (pm20) REVERT: E 42 ARG cc_start: 0.6475 (ttm110) cc_final: 0.6037 (ptm160) REVERT: E 54 ILE cc_start: 0.5031 (OUTLIER) cc_final: 0.4748 (tp) REVERT: E 65 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.5961 (mm) REVERT: E 73 SER cc_start: 0.7469 (OUTLIER) cc_final: 0.7247 (m) REVERT: E 105 ARG cc_start: 0.7804 (ttt-90) cc_final: 0.7573 (ttt-90) REVERT: E 107 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.6863 (t0) REVERT: E 164 MET cc_start: 0.6838 (tpt) cc_final: 0.6156 (ttm) REVERT: E 201 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7421 (t0) REVERT: E 353 GLN cc_start: 0.5409 (OUTLIER) cc_final: 0.5158 (mp10) REVERT: F 82 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7114 (mm) REVERT: F 84 THR cc_start: 0.7800 (m) cc_final: 0.7345 (p) REVERT: F 122 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7418 (mtmp) REVERT: F 170 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.7146 (t0) REVERT: F 183 ASN cc_start: 0.6674 (p0) cc_final: 0.5773 (t0) REVERT: F 198 GLU cc_start: 0.7894 (tt0) cc_final: 0.7350 (mm-30) REVERT: F 275 THR cc_start: 0.8564 (p) cc_final: 0.8261 (t) REVERT: F 276 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7619 (pp20) REVERT: F 375 GLU cc_start: 0.6815 (pp20) cc_final: 0.6190 (mp0) REVERT: F 376 ARG cc_start: 0.5443 (OUTLIER) cc_final: 0.4856 (tpt90) REVERT: F 435 ASN cc_start: 0.7239 (t0) cc_final: 0.6584 (t0) REVERT: F 544 GLU cc_start: 0.4735 (OUTLIER) cc_final: 0.4436 (mm-30) REVERT: I 25 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6540 (mp0) REVERT: I 35 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7085 (tptt) REVERT: I 66 ARG cc_start: 0.7391 (mpp80) cc_final: 0.6997 (mtt90) REVERT: I 141 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7886 (tp) REVERT: I 208 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7270 (mtp180) REVERT: I 209 GLU cc_start: 0.7801 (tp30) cc_final: 0.7123 (mp0) REVERT: I 342 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: J 21 ASP cc_start: 0.8082 (m-30) cc_final: 0.7593 (m-30) REVERT: J 91 ARG cc_start: 0.5918 (tpt170) cc_final: 0.3417 (mtp180) REVERT: J 180 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7536 (p0) REVERT: J 219 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6530 (t0) REVERT: J 294 LYS cc_start: 0.7280 (pttt) cc_final: 0.6675 (mmtp) REVERT: J 311 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8141 (mmmt) REVERT: J 691 MET cc_start: 0.2155 (OUTLIER) cc_final: 0.1529 (mmp) REVERT: M 15 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7146 (mp0) REVERT: M 38 ASN cc_start: 0.8296 (t0) cc_final: 0.7753 (t0) REVERT: M 42 ARG cc_start: 0.7689 (mtm110) cc_final: 0.6870 (mtp180) REVERT: M 211 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8242 (mtpt) REVERT: M 216 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: M 244 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: M 253 GLU cc_start: 0.7723 (tp30) cc_final: 0.7388 (tm-30) REVERT: M 268 LYS cc_start: 0.7623 (mmmm) cc_final: 0.7399 (mmmt) REVERT: M 279 HIS cc_start: 0.5821 (OUTLIER) cc_final: 0.5532 (t-170) REVERT: M 287 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.6306 (m-10) REVERT: M 288 LYS cc_start: 0.6650 (tptp) cc_final: 0.6286 (mmtt) REVERT: M 293 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6669 (tmtt) REVERT: M 319 ARG cc_start: 0.7705 (tmt170) cc_final: 0.7015 (ttm-80) REVERT: M 329 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7612 (t80) REVERT: N 56 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8259 (mp) REVERT: N 69 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7565 (tt0) REVERT: N 110 PHE cc_start: 0.7831 (m-80) cc_final: 0.7429 (m-80) REVERT: N 174 LYS cc_start: 0.7491 (mtpp) cc_final: 0.7271 (ttmt) REVERT: N 188 ASP cc_start: 0.6982 (p0) cc_final: 0.6741 (p0) REVERT: N 260 LYS cc_start: 0.6707 (tmtt) cc_final: 0.6023 (tptp) REVERT: N 263 GLU cc_start: 0.7115 (tt0) cc_final: 0.6381 (mt-10) REVERT: N 375 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: N 379 ASN cc_start: 0.8770 (m-40) cc_final: 0.8506 (m-40) REVERT: N 398 GLU cc_start: 0.6944 (tp30) cc_final: 0.6626 (tt0) REVERT: N 440 LYS cc_start: 0.8785 (ptpp) cc_final: 0.8525 (ptmt) REVERT: N 471 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.5810 (mp0) REVERT: N 531 SER cc_start: 0.6981 (OUTLIER) cc_final: 0.6307 (p) REVERT: N 551 GLN cc_start: 0.6331 (OUTLIER) cc_final: 0.5889 (tm-30) REVERT: N 558 ASN cc_start: 0.7058 (m-40) cc_final: 0.6795 (m-40) REVERT: N 682 ASN cc_start: 0.6746 (OUTLIER) cc_final: 0.6358 (m-40) outliers start: 250 outliers final: 84 residues processed: 568 average time/residue: 0.5433 time to fit residues: 394.6229 Evaluate side-chains 453 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 327 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 31 ARG Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 174 LYS Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 700 THR Chi-restraints excluded: chain F residue 708 LYS Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 160 MET Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 354 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 118 ASN Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 180 ASN Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 219 ASP Chi-restraints excluded: chain J residue 311 LYS Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 371 THR Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 440 LYS Chi-restraints excluded: chain J residue 509 MET Chi-restraints excluded: chain J residue 531 SER Chi-restraints excluded: chain J residue 550 GLU Chi-restraints excluded: chain J residue 691 MET Chi-restraints excluded: chain J residue 698 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain M residue 244 GLU Chi-restraints excluded: chain M residue 251 VAL Chi-restraints excluded: chain M residue 279 HIS Chi-restraints excluded: chain M residue 287 TYR Chi-restraints excluded: chain M residue 293 LYS Chi-restraints excluded: chain M residue 329 TYR Chi-restraints excluded: chain M residue 342 GLU Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 126 SER Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 197 ASP Chi-restraints excluded: chain N residue 356 SER Chi-restraints excluded: chain N residue 375 GLU Chi-restraints excluded: chain N residue 410 SER Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 471 GLU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 531 SER Chi-restraints excluded: chain N residue 551 GLN Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 633 TYR Chi-restraints excluded: chain N residue 682 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 337 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 354 optimal weight: 0.7980 chunk 221 optimal weight: 9.9990 chunk 418 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 322 optimal weight: 30.0000 chunk 258 optimal weight: 2.9990 chunk 359 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN B 26 ASN B 65 ASN B 351 GLN E 113 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN ** F 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 ASN I 68 ASN I 138 GLN J 350 GLN ** J 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 ASN M 138 GLN M 146 ASN ** M 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 433 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.232125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.170187 restraints weight = 50839.373| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.69 r_work: 0.3798 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 43613 Z= 0.206 Angle : 0.624 8.586 60664 Z= 0.346 Chirality : 0.045 0.306 7041 Planarity : 0.004 0.054 6119 Dihedral : 22.889 177.920 10068 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 6.74 % Allowed : 26.02 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.28 (0.13), residues: 3990 helix: 0.84 (0.11), residues: 2068 sheet: -0.18 (0.22), residues: 552 loop : -0.49 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 69 TYR 0.022 0.002 TYR B 704 PHE 0.021 0.002 PHE E 218 TRP 0.010 0.002 TRP F 697 HIS 0.007 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (43613) covalent geometry : angle 0.62381 / 0.35 (60664) hydrogen bonds : bond 0.04900 / 3.20 ( 1958) hydrogen bonds : angle 4.62559 / 3.29 ( 5483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 355 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.4732 (mpp) cc_final: 0.4434 (mpt) REVERT: A 16 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7521 (ttpt) REVERT: A 35 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7045 (pptt) REVERT: A 62 HIS cc_start: 0.5009 (OUTLIER) cc_final: 0.4746 (m90) REVERT: A 69 ARG cc_start: 0.7962 (ttt180) cc_final: 0.7175 (ttm110) REVERT: A 142 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: A 160 MET cc_start: 0.7205 (tpt) cc_final: 0.6886 (mtp) REVERT: A 229 MET cc_start: 0.8040 (mtt) cc_final: 0.7803 (mtt) REVERT: A 315 LYS cc_start: 0.5599 (OUTLIER) cc_final: 0.5091 (ptpt) REVERT: A 329 TYR cc_start: 0.4991 (t80) cc_final: 0.4515 (m-80) REVERT: A 339 PHE cc_start: 0.7596 (t80) cc_final: 0.7286 (t80) REVERT: B 3 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8094 (mp) REVERT: B 89 ASN cc_start: 0.6998 (m-40) cc_final: 0.6211 (p0) REVERT: B 102 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7428 (tttt) REVERT: B 258 SER cc_start: 0.7450 (p) cc_final: 0.7214 (m) REVERT: B 260 LYS cc_start: 0.7539 (tptt) cc_final: 0.7305 (tptm) REVERT: B 286 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: B 359 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7482 (mptt) REVERT: B 375 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: B 414 LEU cc_start: 0.7387 (pt) cc_final: 0.6533 (mt) REVERT: B 440 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8179 (mttm) REVERT: B 473 MET cc_start: 0.1556 (OUTLIER) cc_final: 0.0570 (tmm) REVERT: B 501 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7456 (tp) REVERT: B 551 GLN cc_start: 0.6238 (mp10) cc_final: 0.5583 (pt0) REVERT: B 641 GLU cc_start: 0.4811 (mt-10) cc_final: 0.4411 (mm-30) REVERT: B 690 GLN cc_start: 0.3390 (pm20) cc_final: 0.2665 (tm-30) REVERT: B 736 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7241 (mm-40) REVERT: E 42 ARG cc_start: 0.6442 (ttm110) cc_final: 0.6055 (ptm160) REVERT: E 65 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.5952 (mm) REVERT: E 107 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7008 (t0) REVERT: E 201 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7382 (t0) REVERT: E 288 LYS cc_start: 0.6009 (OUTLIER) cc_final: 0.4976 (tptm) REVERT: F 41 LYS cc_start: 0.8259 (mttt) cc_final: 0.8026 (mttm) REVERT: F 82 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.7070 (mm) REVERT: F 84 THR cc_start: 0.7894 (m) cc_final: 0.7503 (p) REVERT: F 108 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6487 (mp) REVERT: F 122 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7483 (mtmp) REVERT: F 170 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.7079 (m-40) REVERT: F 183 ASN cc_start: 0.6720 (p0) cc_final: 0.5817 (t0) REVERT: F 191 GLU cc_start: 0.7753 (pt0) cc_final: 0.6977 (tp30) REVERT: F 198 GLU cc_start: 0.7848 (tt0) cc_final: 0.7290 (mm-30) REVERT: F 275 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8246 (t) REVERT: F 375 GLU cc_start: 0.6804 (pp20) cc_final: 0.6213 (mp0) REVERT: F 429 VAL cc_start: 0.5685 (OUTLIER) cc_final: 0.5305 (t) REVERT: F 435 ASN cc_start: 0.7272 (t0) cc_final: 0.6686 (t0) REVERT: F 544 GLU cc_start: 0.4868 (OUTLIER) cc_final: 0.4502 (mm-30) REVERT: I 25 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: I 35 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6905 (ttpp) REVERT: I 66 ARG cc_start: 0.7330 (mpp80) cc_final: 0.7024 (mpt90) REVERT: I 67 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6626 (mp) REVERT: I 72 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6962 (mp) REVERT: I 151 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7051 (tm-30) REVERT: I 167 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6814 (ttp-170) REVERT: I 209 GLU cc_start: 0.7879 (tp30) cc_final: 0.7131 (mp0) REVERT: I 338 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7703 (mtpp) REVERT: I 342 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: J 86 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6365 (mmm160) REVERT: J 91 ARG cc_start: 0.5959 (tpt170) cc_final: 0.3469 (mtp180) REVERT: J 180 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7637 (p0) REVERT: J 194 ASN cc_start: 0.7576 (t160) cc_final: 0.7324 (t0) REVERT: J 203 ARG cc_start: 0.5605 (OUTLIER) cc_final: 0.5117 (ttt180) REVERT: J 273 THR cc_start: 0.8271 (m) cc_final: 0.7829 (p) REVERT: J 477 LEU cc_start: 0.4425 (OUTLIER) cc_final: 0.3941 (pp) REVERT: J 691 MET cc_start: 0.2179 (ptp) cc_final: 0.1303 (mmp) REVERT: M 38 ASN cc_start: 0.8286 (t0) cc_final: 0.7780 (t0) REVERT: M 42 ARG cc_start: 0.7680 (mtm110) cc_final: 0.6988 (mtp180) REVERT: M 48 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7565 (t) REVERT: M 216 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: M 244 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: M 253 GLU cc_start: 0.7664 (tp30) cc_final: 0.7384 (tm-30) REVERT: M 279 HIS cc_start: 0.5845 (OUTLIER) cc_final: 0.5585 (t-170) REVERT: M 288 LYS cc_start: 0.6637 (tptp) cc_final: 0.6233 (mmtt) REVERT: M 293 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6676 (tmtt) REVERT: M 319 ARG cc_start: 0.7725 (tmt170) cc_final: 0.7101 (ttm170) REVERT: N 56 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8256 (mp) REVERT: N 102 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8446 (tttp) REVERT: N 110 PHE cc_start: 0.7836 (m-80) cc_final: 0.7462 (m-80) REVERT: N 174 LYS cc_start: 0.7501 (mtpp) cc_final: 0.7225 (ttmt) REVERT: N 219 ASP cc_start: 0.7148 (m-30) cc_final: 0.6917 (m-30) REVERT: N 263 GLU cc_start: 0.7127 (tt0) cc_final: 0.6372 (mt-10) REVERT: N 375 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: N 379 ASN cc_start: 0.8741 (m-40) cc_final: 0.8445 (m-40) REVERT: N 398 GLU cc_start: 0.7077 (tp30) cc_final: 0.6696 (tt0) REVERT: N 440 LYS cc_start: 0.8852 (ptpp) cc_final: 0.8591 (ptmt) REVERT: N 471 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.5804 (mp0) REVERT: N 551 GLN cc_start: 0.6437 (OUTLIER) cc_final: 0.6052 (tm-30) REVERT: N 682 ASN cc_start: 0.6801 (OUTLIER) cc_final: 0.6301 (m-40) REVERT: N 685 PHE cc_start: 0.4770 (OUTLIER) cc_final: 0.4144 (m-80) outliers start: 255 outliers final: 107 residues processed: 558 average time/residue: 0.5180 time to fit residues: 370.5031 Evaluate side-chains 469 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 319 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 708 LYS Chi-restraints excluded: chain F residue 741 ILE Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 160 MET Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 118 ASN Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 180 ASN Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain J residue 203 ARG Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 440 LYS Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain J residue 501 ILE Chi-restraints excluded: chain J residue 509 MET Chi-restraints excluded: chain J residue 531 SER Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 550 GLU Chi-restraints excluded: chain J residue 648 LEU Chi-restraints excluded: chain J residue 674 GLU Chi-restraints excluded: chain J residue 698 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain M residue 244 GLU Chi-restraints excluded: chain M residue 251 VAL Chi-restraints excluded: chain M residue 279 HIS Chi-restraints excluded: chain M residue 293 LYS Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 356 SER Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 375 GLU Chi-restraints excluded: chain N residue 410 SER Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 470 PHE Chi-restraints excluded: chain N residue 471 GLU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 551 GLN Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 682 ASN Chi-restraints excluded: chain N residue 685 PHE Chi-restraints excluded: chain N residue 700 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 425 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 373 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 343 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 403 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN I 138 GLN ** J 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 350 GLN ** J 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 GLN ** M 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN ** N 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 736 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.233598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.172127 restraints weight = 50883.627| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.71 r_work: 0.3825 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 43613 Z= 0.143 Angle : 0.558 8.700 60664 Z= 0.313 Chirality : 0.042 0.300 7041 Planarity : 0.004 0.048 6119 Dihedral : 22.787 177.244 10057 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Rotamer: Outliers : 5.39 % Allowed : 27.71 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.47 (0.13), residues: 3990 helix: 1.05 (0.11), residues: 2069 sheet: -0.21 (0.22), residues: 551 loop : -0.46 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 105 TYR 0.018 0.001 TYR N 47 PHE 0.020 0.001 PHE E 218 TRP 0.009 0.001 TRP B 559 HIS 0.012 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (43613) covalent geometry : angle 0.55831 / 0.31 (60664) hydrogen bonds : bond 0.04286 / 2.78 ( 1958) hydrogen bonds : angle 4.44801 / 3.17 ( 5483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 360 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.4699 (mpp) cc_final: 0.4436 (mpt) REVERT: A 16 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7505 (ttpt) REVERT: A 35 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7045 (pptt) REVERT: A 62 HIS cc_start: 0.5009 (OUTLIER) cc_final: 0.4722 (m90) REVERT: A 69 ARG cc_start: 0.7973 (ttt180) cc_final: 0.7289 (ttm110) REVERT: A 160 MET cc_start: 0.7211 (tpt) cc_final: 0.6928 (mtp) REVERT: A 229 MET cc_start: 0.8048 (mtt) cc_final: 0.7814 (mtp) REVERT: A 253 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6498 (pp20) REVERT: A 315 LYS cc_start: 0.5563 (ptpp) cc_final: 0.5279 (ptpt) REVERT: A 329 TYR cc_start: 0.4918 (t80) cc_final: 0.4347 (m-80) REVERT: B 3 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8058 (mp) REVERT: B 18 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8460 (tp) REVERT: B 89 ASN cc_start: 0.6963 (m-40) cc_final: 0.6215 (p0) REVERT: B 102 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7428 (tttt) REVERT: B 188 ASP cc_start: 0.5966 (p0) cc_final: 0.5699 (t0) REVERT: B 191 GLU cc_start: 0.8176 (tt0) cc_final: 0.7295 (mp0) REVERT: B 258 SER cc_start: 0.7418 (p) cc_final: 0.7182 (m) REVERT: B 359 LYS cc_start: 0.8140 (mmmt) cc_final: 0.7487 (mptt) REVERT: B 375 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: B 440 LYS cc_start: 0.8572 (mtpt) cc_final: 0.8158 (mttm) REVERT: B 551 GLN cc_start: 0.6076 (mp10) cc_final: 0.5417 (pt0) REVERT: B 641 GLU cc_start: 0.4704 (mt-10) cc_final: 0.4321 (mm-30) REVERT: B 690 GLN cc_start: 0.3246 (pm20) cc_final: 0.3023 (mp10) REVERT: B 699 THR cc_start: 0.7985 (m) cc_final: 0.7768 (m) REVERT: B 736 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7231 (mm110) REVERT: E 65 LEU cc_start: 0.6355 (OUTLIER) cc_final: 0.5999 (mm) REVERT: E 107 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7067 (t0) REVERT: E 151 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6427 (mt-10) REVERT: E 164 MET cc_start: 0.6691 (tpt) cc_final: 0.6248 (ttm) REVERT: E 201 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7428 (t0) REVERT: F 41 LYS cc_start: 0.8219 (mttt) cc_final: 0.8013 (mttm) REVERT: F 82 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7179 (mm) REVERT: F 84 THR cc_start: 0.7849 (m) cc_final: 0.7507 (p) REVERT: F 108 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6301 (mp) REVERT: F 122 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7489 (mtmp) REVERT: F 183 ASN cc_start: 0.6733 (p0) cc_final: 0.5906 (t0) REVERT: F 191 GLU cc_start: 0.7717 (pt0) cc_final: 0.6944 (tp30) REVERT: F 275 THR cc_start: 0.8544 (p) cc_final: 0.8276 (t) REVERT: F 308 SER cc_start: 0.7797 (m) cc_final: 0.7424 (p) REVERT: F 375 GLU cc_start: 0.6669 (pp20) cc_final: 0.6143 (mp0) REVERT: F 429 VAL cc_start: 0.5616 (OUTLIER) cc_final: 0.5252 (t) REVERT: F 435 ASN cc_start: 0.7193 (t0) cc_final: 0.6607 (t0) REVERT: F 544 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.4531 (mm-30) REVERT: I 25 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: I 35 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6907 (ttpp) REVERT: I 66 ARG cc_start: 0.7365 (mpp80) cc_final: 0.7071 (mpt90) REVERT: I 72 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6953 (mp) REVERT: I 141 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7869 (tp) REVERT: I 151 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7097 (tm-30) REVERT: I 205 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8520 (m) REVERT: I 209 GLU cc_start: 0.7764 (tp30) cc_final: 0.7057 (mp0) REVERT: J 18 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8159 (mt) REVERT: J 86 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6355 (mmm160) REVERT: J 91 ARG cc_start: 0.5886 (tpt170) cc_final: 0.3399 (mtp180) REVERT: J 180 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7726 (p0) REVERT: J 273 THR cc_start: 0.8195 (m) cc_final: 0.7731 (p) REVERT: J 691 MET cc_start: 0.2185 (OUTLIER) cc_final: 0.1280 (mmp) REVERT: M 38 ASN cc_start: 0.8342 (t0) cc_final: 0.7851 (t0) REVERT: M 42 ARG cc_start: 0.7694 (mtm110) cc_final: 0.7045 (mtp180) REVERT: M 48 SER cc_start: 0.7931 (OUTLIER) cc_final: 0.7566 (t) REVERT: M 164 MET cc_start: 0.8336 (ttp) cc_final: 0.7887 (ttt) REVERT: M 211 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8200 (mtpt) REVERT: M 253 GLU cc_start: 0.7628 (tp30) cc_final: 0.7386 (tm-30) REVERT: M 276 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6965 (mttm) REVERT: M 279 HIS cc_start: 0.5876 (OUTLIER) cc_final: 0.5577 (t-170) REVERT: M 287 TYR cc_start: 0.6717 (m-10) cc_final: 0.6474 (m-10) REVERT: M 288 LYS cc_start: 0.6610 (tptp) cc_final: 0.6249 (mmtt) REVERT: M 319 ARG cc_start: 0.7718 (tmt170) cc_final: 0.7048 (ttm-80) REVERT: N 56 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8190 (mp) REVERT: N 91 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.5746 (tpt90) REVERT: N 174 LYS cc_start: 0.7465 (mtpp) cc_final: 0.7208 (ttmt) REVERT: N 212 ASP cc_start: 0.7442 (m-30) cc_final: 0.6986 (m-30) REVERT: N 219 ASP cc_start: 0.7045 (m-30) cc_final: 0.6844 (m-30) REVERT: N 263 GLU cc_start: 0.7145 (tt0) cc_final: 0.6322 (mt-10) REVERT: N 379 ASN cc_start: 0.8705 (m-40) cc_final: 0.8386 (m-40) REVERT: N 398 GLU cc_start: 0.7076 (tp30) cc_final: 0.6711 (tt0) REVERT: N 440 LYS cc_start: 0.8795 (ptpp) cc_final: 0.8507 (ptmt) REVERT: N 471 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5746 (mp0) REVERT: N 551 GLN cc_start: 0.6283 (OUTLIER) cc_final: 0.5880 (tm-30) REVERT: N 558 ASN cc_start: 0.7001 (m-40) cc_final: 0.6756 (m-40) REVERT: N 680 LYS cc_start: 0.6531 (OUTLIER) cc_final: 0.6176 (tppt) REVERT: N 682 ASN cc_start: 0.6781 (OUTLIER) cc_final: 0.6364 (m-40) REVERT: N 735 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7808 (mm-30) outliers start: 204 outliers final: 86 residues processed: 524 average time/residue: 0.5307 time to fit residues: 356.7167 Evaluate side-chains 442 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 322 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 708 LYS Chi-restraints excluded: chain F residue 741 ILE Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 205 SER Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 118 ASN Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 180 ASN Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 375 GLU Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 448 ILE Chi-restraints excluded: chain J residue 501 ILE Chi-restraints excluded: chain J residue 509 MET Chi-restraints excluded: chain J residue 531 SER Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 550 GLU Chi-restraints excluded: chain J residue 674 GLU Chi-restraints excluded: chain J residue 691 MET Chi-restraints excluded: chain J residue 698 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 251 VAL Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain M residue 279 HIS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 410 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 470 PHE Chi-restraints excluded: chain N residue 471 GLU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 551 GLN Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 633 TYR Chi-restraints excluded: chain N residue 660 LEU Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 682 ASN Chi-restraints excluded: chain N residue 700 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 265 optimal weight: 4.9990 chunk 361 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 374 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 295 optimal weight: 10.0000 chunk 250 optimal weight: 0.0370 chunk 414 optimal weight: 0.9990 chunk 236 optimal weight: 4.9990 chunk 264 optimal weight: 0.7980 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 351 GLN E 113 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 ASN I 138 GLN I 146 ASN J 26 ASN J 350 GLN ** J 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 GLN ** M 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN N 121 ASN ** N 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 736 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.231674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.170337 restraints weight = 50501.379| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.68 r_work: 0.3794 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 43613 Z= 0.187 Angle : 0.586 9.770 60664 Z= 0.324 Chirality : 0.043 0.309 7041 Planarity : 0.004 0.048 6119 Dihedral : 22.744 175.859 10053 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.03 % Favored : 96.87 % Rotamer: Outliers : 6.26 % Allowed : 26.68 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.43 (0.13), residues: 3990 helix: 1.03 (0.11), residues: 2083 sheet: -0.26 (0.22), residues: 551 loop : -0.49 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 105 TYR 0.027 0.002 TYR M 150 PHE 0.024 0.002 PHE E 218 TRP 0.009 0.001 TRP B 559 HIS 0.011 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (43613) covalent geometry : angle 0.58561 / 0.32 (60664) hydrogen bonds : bond 0.04531 / 2.97 ( 1958) hydrogen bonds : angle 4.45817 / 3.17 ( 5483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 342 time to evaluate : 1.286 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: A 6 MET cc_start: 0.4672 (mpp) cc_final: 0.4402 (mpt) REVERT: A 16 LYS cc_start: 0.7840 (ttmm) cc_final: 0.7497 (ttpt) REVERT: A 35 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7058 (pptt) REVERT: A 62 HIS cc_start: 0.4984 (OUTLIER) cc_final: 0.4768 (m90) REVERT: A 69 ARG cc_start: 0.7962 (ttt180) cc_final: 0.7262 (ttm110) REVERT: A 142 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: A 160 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7031 (ttm) REVERT: A 253 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6553 (pm20) REVERT: A 315 LYS cc_start: 0.5650 (ptpp) cc_final: 0.5418 (ptmt) REVERT: A 329 TYR cc_start: 0.4848 (t80) cc_final: 0.4388 (m-80) REVERT: B 24 ASP cc_start: 0.8075 (m-30) cc_final: 0.7846 (m-30) REVERT: B 89 ASN cc_start: 0.7153 (m-40) cc_final: 0.6397 (p0) REVERT: B 102 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7445 (tttt) REVERT: B 191 GLU cc_start: 0.8218 (tt0) cc_final: 0.7299 (mp0) REVERT: B 258 SER cc_start: 0.7423 (p) cc_final: 0.7222 (m) REVERT: B 286 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: B 359 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7514 (mptt) REVERT: B 375 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: B 440 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8229 (mttm) REVERT: B 501 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7447 (tp) REVERT: B 533 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.6788 (mtmm) REVERT: B 551 GLN cc_start: 0.6104 (mp10) cc_final: 0.5455 (pt0) REVERT: B 641 GLU cc_start: 0.4729 (mt-10) cc_final: 0.4344 (mm-30) REVERT: B 690 GLN cc_start: 0.3398 (pm20) cc_final: 0.3103 (mp10) REVERT: B 736 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7296 (mm110) REVERT: E 65 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6258 (mm) REVERT: E 107 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.6827 (t0) REVERT: E 200 ASP cc_start: 0.7735 (p0) cc_final: 0.7081 (p0) REVERT: E 201 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7404 (t0) REVERT: F 18 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7751 (tp) REVERT: F 41 LYS cc_start: 0.8286 (mttt) cc_final: 0.8067 (mttm) REVERT: F 84 THR cc_start: 0.7891 (m) cc_final: 0.7529 (p) REVERT: F 108 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6391 (mp) REVERT: F 122 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7512 (mtmp) REVERT: F 183 ASN cc_start: 0.6663 (p0) cc_final: 0.5813 (t0) REVERT: F 191 GLU cc_start: 0.7696 (pt0) cc_final: 0.6922 (tp30) REVERT: F 275 THR cc_start: 0.8568 (p) cc_final: 0.8305 (t) REVERT: F 308 SER cc_start: 0.7864 (m) cc_final: 0.7489 (p) REVERT: F 375 GLU cc_start: 0.6695 (pp20) cc_final: 0.6208 (mp0) REVERT: F 429 VAL cc_start: 0.5593 (OUTLIER) cc_final: 0.5219 (t) REVERT: F 435 ASN cc_start: 0.7248 (t0) cc_final: 0.6692 (t0) REVERT: F 544 GLU cc_start: 0.4935 (OUTLIER) cc_final: 0.4567 (mm-30) REVERT: I 25 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: I 35 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6757 (tttm) REVERT: I 66 ARG cc_start: 0.7339 (mpp80) cc_final: 0.7036 (mpt90) REVERT: I 72 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7019 (mp) REVERT: I 141 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7890 (tp) REVERT: I 146 ASN cc_start: 0.7921 (m-40) cc_final: 0.7715 (m-40) REVERT: I 151 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6969 (tm-30) REVERT: I 205 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8590 (m) REVERT: I 209 GLU cc_start: 0.7820 (tp30) cc_final: 0.7124 (mp0) REVERT: J 86 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6386 (mmm160) REVERT: J 91 ARG cc_start: 0.5888 (tpt170) cc_final: 0.3428 (mtp180) REVERT: J 203 ARG cc_start: 0.5776 (OUTLIER) cc_final: 0.5321 (ttt180) REVERT: J 273 THR cc_start: 0.8263 (m) cc_final: 0.7828 (p) REVERT: J 370 SER cc_start: 0.7635 (m) cc_final: 0.7260 (p) REVERT: J 440 LYS cc_start: 0.6553 (OUTLIER) cc_final: 0.5731 (ptpp) REVERT: J 691 MET cc_start: 0.2138 (OUTLIER) cc_final: 0.1099 (mmp) REVERT: M 38 ASN cc_start: 0.8403 (t0) cc_final: 0.7780 (t0) REVERT: M 42 ARG cc_start: 0.7655 (mtm110) cc_final: 0.7115 (mtp180) REVERT: M 48 SER cc_start: 0.8106 (OUTLIER) cc_final: 0.7726 (t) REVERT: M 244 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: M 279 HIS cc_start: 0.5881 (OUTLIER) cc_final: 0.5580 (t-170) REVERT: M 287 TYR cc_start: 0.6940 (m-10) cc_final: 0.6701 (m-10) REVERT: M 288 LYS cc_start: 0.6579 (tptp) cc_final: 0.6254 (mmtt) REVERT: M 293 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6386 (tmtt) REVERT: M 319 ARG cc_start: 0.7774 (tmt170) cc_final: 0.7087 (ttm-80) REVERT: N 56 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8230 (mp) REVERT: N 174 LYS cc_start: 0.7511 (mtpp) cc_final: 0.7219 (ttmt) REVERT: N 180 ASN cc_start: 0.7683 (p0) cc_final: 0.7419 (p0) REVERT: N 219 ASP cc_start: 0.7016 (m-30) cc_final: 0.6815 (m-30) REVERT: N 263 GLU cc_start: 0.7262 (tt0) cc_final: 0.6425 (mt-10) REVERT: N 379 ASN cc_start: 0.8737 (m-40) cc_final: 0.8476 (m-40) REVERT: N 398 GLU cc_start: 0.7102 (tp30) cc_final: 0.6751 (tt0) REVERT: N 440 LYS cc_start: 0.8914 (ptpp) cc_final: 0.8681 (ptmt) REVERT: N 471 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.5803 (mp0) REVERT: N 531 SER cc_start: 0.6864 (OUTLIER) cc_final: 0.6214 (p) REVERT: N 558 ASN cc_start: 0.6846 (m-40) cc_final: 0.6606 (m-40) REVERT: N 680 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.6250 (tppt) outliers start: 237 outliers final: 113 residues processed: 537 average time/residue: 0.5167 time to fit residues: 359.6967 Evaluate side-chains 472 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 323 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 534 LEU Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 708 LYS Chi-restraints excluded: chain F residue 741 ILE Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 205 SER Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 354 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 118 ASN Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 163 HIS Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 200 ILE Chi-restraints excluded: chain J residue 203 ARG Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 350 GLN Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 440 LYS Chi-restraints excluded: chain J residue 448 ILE Chi-restraints excluded: chain J residue 501 ILE Chi-restraints excluded: chain J residue 531 SER Chi-restraints excluded: chain J residue 550 GLU Chi-restraints excluded: chain J residue 648 LEU Chi-restraints excluded: chain J residue 674 GLU Chi-restraints excluded: chain J residue 691 MET Chi-restraints excluded: chain J residue 698 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 244 GLU Chi-restraints excluded: chain M residue 251 VAL Chi-restraints excluded: chain M residue 279 HIS Chi-restraints excluded: chain M residue 293 LYS Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 356 SER Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 410 SER Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 470 PHE Chi-restraints excluded: chain N residue 471 GLU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 531 SER Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 682 ASN Chi-restraints excluded: chain N residue 700 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 118 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 148 optimal weight: 0.7980 chunk 278 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 389 optimal weight: 0.8980 chunk 323 optimal weight: 50.0000 chunk 105 optimal weight: 9.9990 chunk 126 optimal weight: 30.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 351 GLN E 113 ASN E 138 GLN ** F 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS I 138 GLN J 180 ASN ** J 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 GLN ** M 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN ** N 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 433 ASN ** N 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 736 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.232851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.171706 restraints weight = 50792.647| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.74 r_work: 0.3790 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 43613 Z= 0.177 Angle : 0.571 9.017 60664 Z= 0.317 Chirality : 0.043 0.326 7041 Planarity : 0.004 0.048 6119 Dihedral : 22.685 176.419 10044 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.91 % Favored : 96.99 % Rotamer: Outliers : 5.86 % Allowed : 27.58 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.41 (0.13), residues: 3990 helix: 1.04 (0.11), residues: 2088 sheet: -0.32 (0.22), residues: 551 loop : -0.53 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 105 TYR 0.028 0.002 TYR E 287 PHE 0.026 0.002 PHE E 218 TRP 0.009 0.001 TRP B 559 HIS 0.007 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (43613) covalent geometry : angle 0.57140 / 0.32 (60664) hydrogen bonds : bond 0.04375 / 2.85 ( 1958) hydrogen bonds : angle 4.43160 / 3.16 ( 5483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 328 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.4686 (mpp) cc_final: 0.4419 (mpt) REVERT: A 16 LYS cc_start: 0.7771 (ttmm) cc_final: 0.7450 (ttpt) REVERT: A 35 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7061 (pptt) REVERT: A 69 ARG cc_start: 0.7954 (ttt180) cc_final: 0.7228 (ttm110) REVERT: A 142 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: A 160 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.7078 (ttm) REVERT: A 253 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6572 (pm20) REVERT: A 315 LYS cc_start: 0.5710 (ptpp) cc_final: 0.5482 (ptmt) REVERT: A 329 TYR cc_start: 0.5055 (t80) cc_final: 0.4462 (m-80) REVERT: B 18 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8420 (tp) REVERT: B 89 ASN cc_start: 0.7212 (m-40) cc_final: 0.6503 (p0) REVERT: B 188 ASP cc_start: 0.6781 (t0) cc_final: 0.6141 (t0) REVERT: B 191 GLU cc_start: 0.8182 (tt0) cc_final: 0.7269 (mp0) REVERT: B 286 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: B 359 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7507 (mptt) REVERT: B 375 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: B 440 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8286 (mttm) REVERT: B 501 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7471 (tp) REVERT: B 533 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.6781 (mtmm) REVERT: B 551 GLN cc_start: 0.6109 (mp10) cc_final: 0.5467 (pt0) REVERT: B 641 GLU cc_start: 0.4770 (mt-10) cc_final: 0.4312 (mm-30) REVERT: B 690 GLN cc_start: 0.3319 (pm20) cc_final: 0.2982 (mp10) REVERT: B 722 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6965 (mtmt) REVERT: B 736 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7302 (mm110) REVERT: E 65 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6299 (mm) REVERT: E 107 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.6929 (t0) REVERT: E 151 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6403 (mt-10) REVERT: E 200 ASP cc_start: 0.7767 (p0) cc_final: 0.7169 (p0) REVERT: E 342 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6312 (tt0) REVERT: E 353 GLN cc_start: 0.5340 (OUTLIER) cc_final: 0.5103 (mp10) REVERT: F 18 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7669 (tp) REVERT: F 41 LYS cc_start: 0.8272 (mttt) cc_final: 0.8040 (mttm) REVERT: F 84 THR cc_start: 0.7928 (m) cc_final: 0.7578 (p) REVERT: F 108 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6455 (mp) REVERT: F 122 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7545 (mtmp) REVERT: F 183 ASN cc_start: 0.6644 (p0) cc_final: 0.5787 (t0) REVERT: F 191 GLU cc_start: 0.7729 (pt0) cc_final: 0.6918 (tp30) REVERT: F 275 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8321 (t) REVERT: F 375 GLU cc_start: 0.6673 (pp20) cc_final: 0.6208 (mp0) REVERT: F 429 VAL cc_start: 0.5649 (OUTLIER) cc_final: 0.5274 (t) REVERT: F 435 ASN cc_start: 0.7231 (t0) cc_final: 0.6661 (t0) REVERT: F 544 GLU cc_start: 0.4948 (OUTLIER) cc_final: 0.4601 (mm-30) REVERT: F 550 GLU cc_start: 0.4400 (OUTLIER) cc_final: 0.3797 (mt-10) REVERT: I 25 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: I 35 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6778 (ttpp) REVERT: I 66 ARG cc_start: 0.7369 (mpp80) cc_final: 0.7062 (mpt90) REVERT: I 72 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6999 (mp) REVERT: I 141 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7931 (tp) REVERT: I 151 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6970 (tm-30) REVERT: I 209 GLU cc_start: 0.7742 (tp30) cc_final: 0.7050 (mp0) REVERT: I 342 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: J 86 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6373 (mmm160) REVERT: J 91 ARG cc_start: 0.5955 (tpt170) cc_final: 0.3479 (mtp180) REVERT: J 191 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6835 (mm-30) REVERT: J 203 ARG cc_start: 0.5776 (OUTLIER) cc_final: 0.5311 (ttt180) REVERT: J 360 ASP cc_start: 0.7642 (p0) cc_final: 0.7094 (m-30) REVERT: J 440 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.5774 (ptpp) REVERT: J 691 MET cc_start: 0.2047 (OUTLIER) cc_final: 0.0869 (mmp) REVERT: M 38 ASN cc_start: 0.8379 (t0) cc_final: 0.7833 (t0) REVERT: M 42 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7006 (mtp180) REVERT: M 48 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7646 (t) REVERT: M 211 LYS cc_start: 0.8466 (mtpp) cc_final: 0.8213 (mtpt) REVERT: M 244 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: M 288 LYS cc_start: 0.6586 (tptp) cc_final: 0.6277 (mmtt) REVERT: M 293 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6388 (tmtt) REVERT: M 319 ARG cc_start: 0.7778 (tmt170) cc_final: 0.7129 (ttm-80) REVERT: N 56 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8226 (mp) REVERT: N 174 LYS cc_start: 0.7521 (mtpp) cc_final: 0.7233 (ttmt) REVERT: N 180 ASN cc_start: 0.7699 (p0) cc_final: 0.7419 (p0) REVERT: N 263 GLU cc_start: 0.7243 (tt0) cc_final: 0.6452 (mt-10) REVERT: N 398 GLU cc_start: 0.7126 (tp30) cc_final: 0.6780 (tt0) REVERT: N 440 LYS cc_start: 0.8897 (ptpp) cc_final: 0.8667 (ptmt) REVERT: N 471 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.5751 (mp0) REVERT: N 531 SER cc_start: 0.6835 (OUTLIER) cc_final: 0.6172 (p) REVERT: N 558 ASN cc_start: 0.6836 (m-40) cc_final: 0.6633 (m-40) REVERT: N 680 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6201 (tppt) REVERT: N 685 PHE cc_start: 0.4858 (OUTLIER) cc_final: 0.4248 (m-80) REVERT: N 735 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7787 (mm-30) outliers start: 222 outliers final: 114 residues processed: 512 average time/residue: 0.5265 time to fit residues: 347.1576 Evaluate side-chains 468 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 313 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 170 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 722 LYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 550 GLU Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 690 GLN Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 708 LYS Chi-restraints excluded: chain F residue 741 ILE Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 354 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 118 ASN Chi-restraints excluded: chain J residue 136 SER Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 203 ARG Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 440 LYS Chi-restraints excluded: chain J residue 448 ILE Chi-restraints excluded: chain J residue 501 ILE Chi-restraints excluded: chain J residue 531 SER Chi-restraints excluded: chain J residue 550 GLU Chi-restraints excluded: chain J residue 648 LEU Chi-restraints excluded: chain J residue 674 GLU Chi-restraints excluded: chain J residue 691 MET Chi-restraints excluded: chain J residue 698 VAL Chi-restraints excluded: chain J residue 699 THR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 244 GLU Chi-restraints excluded: chain M residue 251 VAL Chi-restraints excluded: chain M residue 293 LYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 351 ILE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 356 SER Chi-restraints excluded: chain N residue 410 SER Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 471 GLU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 531 SER Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 633 TYR Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 682 ASN Chi-restraints excluded: chain N residue 685 PHE Chi-restraints excluded: chain N residue 700 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 92 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 355 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 364 optimal weight: 0.4980 chunk 385 optimal weight: 0.1980 chunk 280 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 281 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN B 189 HIS E 113 ASN E 138 GLN ** F 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 GLN J 180 ASN ** J 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 350 GLN ** J 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 528 ASN M 138 GLN ** M 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN ** N 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 736 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.234477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.173787 restraints weight = 50576.783| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.75 r_work: 0.3816 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 43613 Z= 0.130 Angle : 0.538 8.871 60664 Z= 0.300 Chirality : 0.041 0.306 7041 Planarity : 0.004 0.048 6119 Dihedral : 22.607 179.665 10044 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.07 % Rotamer: Outliers : 5.20 % Allowed : 28.08 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.57 (0.13), residues: 3990 helix: 1.18 (0.11), residues: 2088 sheet: -0.26 (0.22), residues: 551 loop : -0.48 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 42 TYR 0.022 0.001 TYR E 52 PHE 0.026 0.001 PHE F 184 TRP 0.009 0.001 TRP B 559 HIS 0.008 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (43613) covalent geometry : angle 0.53816 / 0.30 (60664) hydrogen bonds : bond 0.04041 / 2.62 ( 1958) hydrogen bonds : angle 4.32595 / 3.08 ( 5483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 347 time to evaluate : 1.276 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: A 6 MET cc_start: 0.4505 (mpp) cc_final: 0.4258 (mpt) REVERT: A 16 LYS cc_start: 0.7735 (ttmm) cc_final: 0.7408 (ttpt) REVERT: A 30 GLN cc_start: 0.6535 (mm110) cc_final: 0.5316 (mm-40) REVERT: A 35 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7071 (pptt) REVERT: A 69 ARG cc_start: 0.7929 (ttt180) cc_final: 0.7178 (ttm110) REVERT: A 140 LEU cc_start: 0.7719 (tt) cc_final: 0.7517 (tp) REVERT: A 142 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7305 (m-30) REVERT: A 160 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6900 (ttm) REVERT: A 329 TYR cc_start: 0.5014 (t80) cc_final: 0.4427 (m-80) REVERT: B 18 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8443 (tp) REVERT: B 89 ASN cc_start: 0.7154 (m-40) cc_final: 0.6452 (p0) REVERT: B 188 ASP cc_start: 0.6807 (t0) cc_final: 0.6170 (t0) REVERT: B 191 GLU cc_start: 0.8124 (tt0) cc_final: 0.7231 (mp0) REVERT: B 208 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7313 (tptt) REVERT: B 286 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: B 359 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7459 (mptt) REVERT: B 375 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: B 440 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8210 (mttm) REVERT: B 501 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7485 (tp) REVERT: B 533 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.6765 (mtmm) REVERT: B 551 GLN cc_start: 0.6253 (mp10) cc_final: 0.5553 (pt0) REVERT: B 641 GLU cc_start: 0.4741 (mt-10) cc_final: 0.4310 (mm-30) REVERT: B 690 GLN cc_start: 0.3227 (pm20) cc_final: 0.2908 (mp10) REVERT: B 736 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7172 (mm110) REVERT: E 65 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6358 (mm) REVERT: E 107 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.6928 (t0) REVERT: E 151 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6425 (mt-10) REVERT: E 200 ASP cc_start: 0.7696 (p0) cc_final: 0.7115 (p0) REVERT: E 342 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6379 (tt0) REVERT: E 353 GLN cc_start: 0.5274 (OUTLIER) cc_final: 0.5058 (mp10) REVERT: F 18 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7609 (tp) REVERT: F 84 THR cc_start: 0.7880 (m) cc_final: 0.7562 (p) REVERT: F 108 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6419 (mp) REVERT: F 122 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7475 (mtmp) REVERT: F 183 ASN cc_start: 0.6561 (p0) cc_final: 0.5781 (t0) REVERT: F 191 GLU cc_start: 0.7662 (pt0) cc_final: 0.6873 (tp30) REVERT: F 275 THR cc_start: 0.8555 (p) cc_final: 0.8314 (t) REVERT: F 308 SER cc_start: 0.7825 (m) cc_final: 0.7436 (p) REVERT: F 375 GLU cc_start: 0.6624 (pp20) cc_final: 0.6204 (mp0) REVERT: F 429 VAL cc_start: 0.5580 (OUTLIER) cc_final: 0.5222 (t) REVERT: F 435 ASN cc_start: 0.7121 (t0) cc_final: 0.6560 (t0) REVERT: F 544 GLU cc_start: 0.4941 (OUTLIER) cc_final: 0.4579 (mm-30) REVERT: I 25 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6235 (mp0) REVERT: I 35 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6697 (ttpp) REVERT: I 66 ARG cc_start: 0.7362 (mpp80) cc_final: 0.7083 (mpt90) REVERT: I 72 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6961 (mp) REVERT: I 151 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6910 (tm-30) REVERT: I 209 GLU cc_start: 0.7683 (tp30) cc_final: 0.7036 (mp0) REVERT: I 342 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: J 86 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6333 (mmm160) REVERT: J 91 ARG cc_start: 0.5824 (tpt170) cc_final: 0.3408 (mtp180) REVERT: J 191 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6897 (mm-30) REVERT: J 203 ARG cc_start: 0.5741 (OUTLIER) cc_final: 0.5254 (ttt180) REVERT: J 375 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6115 (tp30) REVERT: M 38 ASN cc_start: 0.8342 (t0) cc_final: 0.7793 (t0) REVERT: M 42 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7034 (mtp180) REVERT: M 50 ILE cc_start: 0.8546 (mm) cc_final: 0.8171 (mm) REVERT: M 211 LYS cc_start: 0.8440 (mtpp) cc_final: 0.8192 (mtpt) REVERT: M 253 GLU cc_start: 0.7590 (tp30) cc_final: 0.7304 (tm-30) REVERT: M 288 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.6288 (mmtt) REVERT: M 293 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6264 (tmtt) REVERT: M 361 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6839 (tt) REVERT: N 56 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8152 (mp) REVERT: N 91 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.5756 (tpt90) REVERT: N 174 LYS cc_start: 0.7436 (mtpp) cc_final: 0.7156 (ttmt) REVERT: N 180 ASN cc_start: 0.7686 (p0) cc_final: 0.7409 (p0) REVERT: N 212 ASP cc_start: 0.7462 (m-30) cc_final: 0.6988 (m-30) REVERT: N 263 GLU cc_start: 0.7244 (tt0) cc_final: 0.6436 (mt-10) REVERT: N 379 ASN cc_start: 0.8613 (m-40) cc_final: 0.8306 (m-40) REVERT: N 398 GLU cc_start: 0.7011 (tp30) cc_final: 0.6673 (tt0) REVERT: N 440 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8588 (ptmt) REVERT: N 471 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.5738 (mp0) REVERT: N 558 ASN cc_start: 0.6818 (m-40) cc_final: 0.6606 (m-40) REVERT: N 680 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.6142 (tppt) REVERT: N 685 PHE cc_start: 0.4866 (OUTLIER) cc_final: 0.4272 (m-80) outliers start: 197 outliers final: 98 residues processed: 513 average time/residue: 0.5259 time to fit residues: 349.1142 Evaluate side-chains 454 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 322 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 690 GLN Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 708 LYS Chi-restraints excluded: chain F residue 741 ILE Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 118 ASN Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 203 ARG Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 350 GLN Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 501 ILE Chi-restraints excluded: chain J residue 531 SER Chi-restraints excluded: chain J residue 550 GLU Chi-restraints excluded: chain J residue 648 LEU Chi-restraints excluded: chain J residue 674 GLU Chi-restraints excluded: chain J residue 691 MET Chi-restraints excluded: chain J residue 698 VAL Chi-restraints excluded: chain J residue 699 THR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 251 VAL Chi-restraints excluded: chain M residue 288 LYS Chi-restraints excluded: chain M residue 293 LYS Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 126 SER Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 410 SER Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 471 GLU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 633 TYR Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 685 PHE Chi-restraints excluded: chain N residue 700 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 136 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 279 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 217 optimal weight: 20.0000 chunk 263 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS E 113 ASN E 138 GLN ** F 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 GLN J 180 ASN ** J 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 GLN ** M 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN ** N 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 736 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.234507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.173897 restraints weight = 50529.598| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.70 r_work: 0.3820 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 43613 Z= 0.135 Angle : 0.537 9.392 60664 Z= 0.299 Chirality : 0.041 0.308 7041 Planarity : 0.004 0.046 6119 Dihedral : 22.551 179.738 10044 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.91 % Favored : 96.99 % Rotamer: Outliers : 4.94 % Allowed : 28.42 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.59 (0.13), residues: 3990 helix: 1.21 (0.11), residues: 2088 sheet: -0.26 (0.22), residues: 551 loop : -0.48 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 532 TYR 0.031 0.001 TYR A 150 PHE 0.030 0.001 PHE F 184 TRP 0.010 0.001 TRP B 559 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (43613) covalent geometry : angle 0.53705 / 0.30 (60664) hydrogen bonds : bond 0.04024 / 2.61 ( 1958) hydrogen bonds : angle 4.29150 / 3.06 ( 5483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 338 time to evaluate : 1.272 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: A 6 MET cc_start: 0.4540 (mpp) cc_final: 0.4317 (mpt) REVERT: A 16 LYS cc_start: 0.7749 (ttmm) cc_final: 0.7419 (ttpt) REVERT: A 30 GLN cc_start: 0.6542 (mm110) cc_final: 0.5330 (mm-40) REVERT: A 35 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7027 (pptt) REVERT: A 69 ARG cc_start: 0.7949 (ttt180) cc_final: 0.7180 (ttm110) REVERT: A 139 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.6342 (mttt) REVERT: A 140 LEU cc_start: 0.7683 (tt) cc_final: 0.7480 (tp) REVERT: A 142 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: A 160 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6979 (ttm) REVERT: A 324 ASN cc_start: 0.6638 (m110) cc_final: 0.6247 (m-40) REVERT: A 329 TYR cc_start: 0.5075 (t80) cc_final: 0.4389 (m-80) REVERT: B 18 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8443 (tp) REVERT: B 89 ASN cc_start: 0.7173 (m-40) cc_final: 0.6516 (p0) REVERT: B 188 ASP cc_start: 0.6846 (t0) cc_final: 0.6507 (t70) REVERT: B 191 GLU cc_start: 0.8141 (tt0) cc_final: 0.7246 (mp0) REVERT: B 208 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7335 (tptt) REVERT: B 286 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: B 359 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7467 (mptt) REVERT: B 375 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: B 440 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8244 (mttm) REVERT: B 501 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7470 (tp) REVERT: B 533 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6748 (mtmm) REVERT: B 551 GLN cc_start: 0.6302 (mp10) cc_final: 0.5558 (pt0) REVERT: B 641 GLU cc_start: 0.4727 (mt-10) cc_final: 0.4275 (mm-30) REVERT: B 690 GLN cc_start: 0.3364 (pm20) cc_final: 0.3048 (mp10) REVERT: B 736 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7107 (mm110) REVERT: E 65 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6534 (mt) REVERT: E 107 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.6975 (t0) REVERT: E 151 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6441 (mt-10) REVERT: E 200 ASP cc_start: 0.7617 (p0) cc_final: 0.7075 (p0) REVERT: E 342 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6381 (tt0) REVERT: F 84 THR cc_start: 0.7895 (m) cc_final: 0.7563 (p) REVERT: F 108 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6451 (mp) REVERT: F 122 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7507 (mtmp) REVERT: F 183 ASN cc_start: 0.6604 (p0) cc_final: 0.5814 (t0) REVERT: F 191 GLU cc_start: 0.7692 (pt0) cc_final: 0.6894 (tp30) REVERT: F 275 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8313 (t) REVERT: F 308 SER cc_start: 0.7811 (m) cc_final: 0.7431 (p) REVERT: F 375 GLU cc_start: 0.6611 (pp20) cc_final: 0.6235 (mp0) REVERT: F 429 VAL cc_start: 0.5621 (OUTLIER) cc_final: 0.5252 (t) REVERT: F 435 ASN cc_start: 0.7126 (t0) cc_final: 0.6530 (t0) REVERT: F 544 GLU cc_start: 0.4991 (OUTLIER) cc_final: 0.4482 (mm-30) REVERT: F 550 GLU cc_start: 0.4415 (OUTLIER) cc_final: 0.3820 (mt-10) REVERT: I 25 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6230 (mp0) REVERT: I 35 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6754 (ttpp) REVERT: I 66 ARG cc_start: 0.7363 (mpp80) cc_final: 0.7065 (mpt90) REVERT: I 72 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.6946 (mp) REVERT: I 141 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7885 (tp) REVERT: I 151 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6939 (tm-30) REVERT: I 209 GLU cc_start: 0.7633 (tp30) cc_final: 0.7005 (mp0) REVERT: I 342 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: J 18 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8228 (mt) REVERT: J 86 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6346 (mmm160) REVERT: J 91 ARG cc_start: 0.5919 (tpt170) cc_final: 0.3504 (mtp180) REVERT: J 191 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6914 (mm-30) REVERT: J 203 ARG cc_start: 0.5755 (OUTLIER) cc_final: 0.5262 (ttt180) REVERT: J 348 LYS cc_start: 0.8047 (pttp) cc_final: 0.7714 (pptt) REVERT: J 360 ASP cc_start: 0.7536 (p0) cc_final: 0.7074 (m-30) REVERT: J 375 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6080 (tp30) REVERT: J 440 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.5740 (ptpp) REVERT: M 38 ASN cc_start: 0.8292 (t0) cc_final: 0.7779 (t0) REVERT: M 42 ARG cc_start: 0.7561 (mtm110) cc_final: 0.7039 (mtp180) REVERT: M 50 ILE cc_start: 0.8544 (mm) cc_final: 0.8202 (mm) REVERT: M 211 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8193 (mtpt) REVERT: M 288 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6287 (mmtt) REVERT: M 293 LYS cc_start: 0.6810 (OUTLIER) cc_final: 0.6252 (tmtt) REVERT: M 361 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6850 (tt) REVERT: N 56 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8148 (mp) REVERT: N 91 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.5765 (tpt90) REVERT: N 122 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8272 (mtpt) REVERT: N 174 LYS cc_start: 0.7449 (mtpp) cc_final: 0.7164 (ttmt) REVERT: N 180 ASN cc_start: 0.7710 (p0) cc_final: 0.7439 (p0) REVERT: N 212 ASP cc_start: 0.7442 (m-30) cc_final: 0.6974 (m-30) REVERT: N 263 GLU cc_start: 0.7221 (tt0) cc_final: 0.6436 (mt-10) REVERT: N 398 GLU cc_start: 0.7025 (tp30) cc_final: 0.6695 (tt0) REVERT: N 422 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7678 (p0) REVERT: N 440 LYS cc_start: 0.8817 (ptpp) cc_final: 0.8578 (ptmt) REVERT: N 471 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.5740 (mp0) REVERT: N 531 SER cc_start: 0.6753 (OUTLIER) cc_final: 0.6160 (p) REVERT: N 551 GLN cc_start: 0.6360 (OUTLIER) cc_final: 0.6033 (tm-30) REVERT: N 558 ASN cc_start: 0.6638 (m-40) cc_final: 0.6371 (m-40) REVERT: N 680 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6142 (tppt) REVERT: N 683 GLU cc_start: 0.5312 (OUTLIER) cc_final: 0.4335 (tm-30) REVERT: N 685 PHE cc_start: 0.4875 (OUTLIER) cc_final: 0.4311 (m-80) outliers start: 187 outliers final: 95 residues processed: 490 average time/residue: 0.5186 time to fit residues: 326.7857 Evaluate side-chains 457 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 319 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 550 GLU Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 690 GLN Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 708 LYS Chi-restraints excluded: chain F residue 741 ILE Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 203 ARG Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 440 LYS Chi-restraints excluded: chain J residue 448 ILE Chi-restraints excluded: chain J residue 501 ILE Chi-restraints excluded: chain J residue 531 SER Chi-restraints excluded: chain J residue 550 GLU Chi-restraints excluded: chain J residue 648 LEU Chi-restraints excluded: chain J residue 674 GLU Chi-restraints excluded: chain J residue 691 MET Chi-restraints excluded: chain J residue 698 VAL Chi-restraints excluded: chain J residue 699 THR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 251 VAL Chi-restraints excluded: chain M residue 288 LYS Chi-restraints excluded: chain M residue 293 LYS Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 410 SER Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 422 ASP Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 471 GLU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 531 SER Chi-restraints excluded: chain N residue 551 GLN Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 683 GLU Chi-restraints excluded: chain N residue 685 PHE Chi-restraints excluded: chain N residue 700 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 10 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 282 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 411 optimal weight: 0.6980 chunk 371 optimal weight: 0.7980 chunk 297 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 223 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN E 113 ASN E 138 GLN ** F 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 GLN ** M 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN ** N 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 558 ASN N 736 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.234588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.173715 restraints weight = 50770.107| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.76 r_work: 0.3817 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43613 Z= 0.135 Angle : 0.539 9.667 60664 Z= 0.299 Chirality : 0.041 0.311 7041 Planarity : 0.004 0.064 6119 Dihedral : 22.466 178.645 10042 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.94 % Rotamer: Outliers : 4.62 % Allowed : 28.79 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.63 (0.13), residues: 3990 helix: 1.24 (0.11), residues: 2088 sheet: -0.23 (0.22), residues: 551 loop : -0.47 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 42 TYR 0.026 0.001 TYR A 150 PHE 0.026 0.001 PHE F 184 TRP 0.010 0.001 TRP B 559 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (43613) covalent geometry : angle 0.53868 / 0.30 (60664) hydrogen bonds : bond 0.03979 / 2.59 ( 1958) hydrogen bonds : angle 4.26771 / 3.04 ( 5483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 337 time to evaluate : 1.476 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: A 6 MET cc_start: 0.4545 (mpp) cc_final: 0.4317 (mpt) REVERT: A 16 LYS cc_start: 0.7760 (ttmm) cc_final: 0.7428 (ttpt) REVERT: A 30 GLN cc_start: 0.6547 (mm110) cc_final: 0.5367 (mm-40) REVERT: A 35 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7024 (pptt) REVERT: A 69 ARG cc_start: 0.7936 (ttt180) cc_final: 0.7156 (ttm110) REVERT: A 139 LYS cc_start: 0.6611 (OUTLIER) cc_final: 0.6294 (mttt) REVERT: A 142 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: A 160 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6820 (ttm) REVERT: A 324 ASN cc_start: 0.6635 (m110) cc_final: 0.6234 (m-40) REVERT: A 329 TYR cc_start: 0.5092 (t80) cc_final: 0.4381 (m-80) REVERT: B 15 ASP cc_start: 0.7930 (t0) cc_final: 0.7647 (p0) REVERT: B 18 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8451 (tp) REVERT: B 89 ASN cc_start: 0.7179 (m-40) cc_final: 0.6508 (p0) REVERT: B 188 ASP cc_start: 0.6961 (t0) cc_final: 0.6632 (t70) REVERT: B 191 GLU cc_start: 0.8109 (tt0) cc_final: 0.7282 (mp0) REVERT: B 208 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7350 (tptt) REVERT: B 285 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: B 286 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: B 311 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7660 (tptp) REVERT: B 359 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7465 (mptt) REVERT: B 375 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: B 440 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8232 (mttm) REVERT: B 501 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7461 (tp) REVERT: B 533 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6728 (mtmm) REVERT: B 551 GLN cc_start: 0.6307 (mp10) cc_final: 0.5523 (pt0) REVERT: B 641 GLU cc_start: 0.4715 (mt-10) cc_final: 0.4279 (mm-30) REVERT: B 690 GLN cc_start: 0.3252 (pm20) cc_final: 0.2925 (mp10) REVERT: B 736 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7032 (mm-40) REVERT: E 65 LEU cc_start: 0.6827 (mm) cc_final: 0.6371 (mm) REVERT: E 107 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7000 (t0) REVERT: E 200 ASP cc_start: 0.7621 (p0) cc_final: 0.7069 (p0) REVERT: F 84 THR cc_start: 0.7855 (m) cc_final: 0.7521 (p) REVERT: F 108 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6426 (mp) REVERT: F 122 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7523 (mtmp) REVERT: F 183 ASN cc_start: 0.6680 (p0) cc_final: 0.5864 (t0) REVERT: F 191 GLU cc_start: 0.7717 (pt0) cc_final: 0.6884 (tp30) REVERT: F 275 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8329 (t) REVERT: F 308 SER cc_start: 0.7784 (m) cc_final: 0.7426 (p) REVERT: F 375 GLU cc_start: 0.6610 (pp20) cc_final: 0.6258 (mp0) REVERT: F 429 VAL cc_start: 0.5593 (OUTLIER) cc_final: 0.5233 (t) REVERT: F 435 ASN cc_start: 0.7089 (t0) cc_final: 0.6494 (t0) REVERT: F 544 GLU cc_start: 0.5053 (OUTLIER) cc_final: 0.4509 (mm-30) REVERT: F 550 GLU cc_start: 0.4403 (OUTLIER) cc_final: 0.4014 (mt-10) REVERT: I 25 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6192 (mp0) REVERT: I 35 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6768 (ttpp) REVERT: I 66 ARG cc_start: 0.7346 (mpp80) cc_final: 0.7075 (mpt90) REVERT: I 72 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6949 (mp) REVERT: I 141 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7872 (tp) REVERT: I 151 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6964 (tm-30) REVERT: I 205 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8541 (m) REVERT: I 209 GLU cc_start: 0.7595 (tp30) cc_final: 0.7045 (mp0) REVERT: I 342 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: J 18 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8241 (mt) REVERT: J 86 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.6372 (mmm160) REVERT: J 91 ARG cc_start: 0.5892 (tpt170) cc_final: 0.3463 (mtp180) REVERT: J 191 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: J 203 ARG cc_start: 0.5758 (OUTLIER) cc_final: 0.5255 (ttt180) REVERT: J 348 LYS cc_start: 0.8158 (pttp) cc_final: 0.7949 (pptt) REVERT: J 440 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.5742 (ptpp) REVERT: M 38 ASN cc_start: 0.8311 (t0) cc_final: 0.7860 (t0) REVERT: M 42 ARG cc_start: 0.7508 (mtm110) cc_final: 0.6984 (mtp180) REVERT: M 50 ILE cc_start: 0.8504 (mm) cc_final: 0.8139 (mm) REVERT: M 55 ASN cc_start: 0.7629 (t0) cc_final: 0.7289 (t0) REVERT: M 211 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8195 (mtpt) REVERT: M 288 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.6307 (mmtt) REVERT: M 293 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.6262 (tptm) REVERT: M 361 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6838 (tt) REVERT: N 56 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8148 (mp) REVERT: N 91 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.5762 (tpt90) REVERT: N 122 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8254 (mtpt) REVERT: N 174 LYS cc_start: 0.7422 (mtpp) cc_final: 0.7151 (ttmt) REVERT: N 180 ASN cc_start: 0.7670 (p0) cc_final: 0.7397 (p0) REVERT: N 212 ASP cc_start: 0.7442 (m-30) cc_final: 0.6986 (m-30) REVERT: N 263 GLU cc_start: 0.7216 (tt0) cc_final: 0.6377 (mt-10) REVERT: N 398 GLU cc_start: 0.7001 (tp30) cc_final: 0.6690 (tt0) REVERT: N 422 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7685 (p0) REVERT: N 440 LYS cc_start: 0.8832 (ptpp) cc_final: 0.8585 (ptmt) REVERT: N 471 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.5708 (mp0) REVERT: N 531 SER cc_start: 0.6719 (OUTLIER) cc_final: 0.6120 (p) REVERT: N 551 GLN cc_start: 0.6325 (OUTLIER) cc_final: 0.5989 (tm-30) REVERT: N 558 ASN cc_start: 0.6802 (OUTLIER) cc_final: 0.6440 (m-40) REVERT: N 680 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.6139 (tppt) REVERT: N 685 PHE cc_start: 0.4883 (OUTLIER) cc_final: 0.4328 (m-80) outliers start: 175 outliers final: 99 residues processed: 480 average time/residue: 0.5931 time to fit residues: 365.6037 Evaluate side-chains 461 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 319 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 550 GLU Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 690 GLN Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 741 ILE Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 129 LYS Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain I residue 205 SER Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 203 ARG Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 440 LYS Chi-restraints excluded: chain J residue 501 ILE Chi-restraints excluded: chain J residue 531 SER Chi-restraints excluded: chain J residue 550 GLU Chi-restraints excluded: chain J residue 648 LEU Chi-restraints excluded: chain J residue 674 GLU Chi-restraints excluded: chain J residue 691 MET Chi-restraints excluded: chain J residue 698 VAL Chi-restraints excluded: chain J residue 699 THR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 251 VAL Chi-restraints excluded: chain M residue 288 LYS Chi-restraints excluded: chain M residue 293 LYS Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 126 SER Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 410 SER Chi-restraints excluded: chain N residue 422 ASP Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 471 GLU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 531 SER Chi-restraints excluded: chain N residue 551 GLN Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 558 ASN Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 685 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 117 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 343 optimal weight: 4.9990 chunk 270 optimal weight: 0.8980 chunk 196 optimal weight: 0.3980 chunk 259 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN E 113 ASN E 138 GLN ** F 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 GLN ** M 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN ** N 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 736 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.234755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.174006 restraints weight = 50876.663| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.82 r_work: 0.3818 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 43613 Z= 0.133 Angle : 0.540 10.025 60664 Z= 0.300 Chirality : 0.041 0.311 7041 Planarity : 0.004 0.045 6119 Dihedral : 22.421 177.914 10042 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.94 % Rotamer: Outliers : 4.33 % Allowed : 28.95 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.63 (0.13), residues: 3990 helix: 1.22 (0.11), residues: 2086 sheet: -0.20 (0.22), residues: 551 loop : -0.45 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 105 TYR 0.026 0.001 TYR A 150 PHE 0.037 0.001 PHE F 184 TRP 0.012 0.001 TRP N 559 HIS 0.013 0.001 HIS I 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (43613) covalent geometry : angle 0.54023 / 0.30 (60664) hydrogen bonds : bond 0.03966 / 2.57 ( 1958) hydrogen bonds : angle 4.25512 / 3.03 ( 5483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7980 Ramachandran restraints generated. 3990 Oldfield, 0 Emsley, 3990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 328 time to evaluate : 1.392 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 revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7754 (ttmm) cc_final: 0.7377 (ttpt) REVERT: A 30 GLN cc_start: 0.6500 (mm110) cc_final: 0.5338 (mm-40) REVERT: A 35 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7042 (pptt) REVERT: A 69 ARG cc_start: 0.7911 (ttt180) cc_final: 0.7149 (ttm110) REVERT: A 142 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7203 (m-30) REVERT: A 160 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6819 (ttm) REVERT: A 324 ASN cc_start: 0.6603 (m110) cc_final: 0.6200 (m-40) REVERT: A 329 TYR cc_start: 0.5084 (t80) cc_final: 0.4364 (m-80) REVERT: B 15 ASP cc_start: 0.7944 (t0) cc_final: 0.7648 (p0) REVERT: B 18 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8457 (tp) REVERT: B 89 ASN cc_start: 0.7165 (m-40) cc_final: 0.6506 (p0) REVERT: B 188 ASP cc_start: 0.6923 (t0) cc_final: 0.6574 (t70) REVERT: B 191 GLU cc_start: 0.8094 (tt0) cc_final: 0.7247 (mp0) REVERT: B 208 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7352 (tptt) REVERT: B 285 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7223 (m-30) REVERT: B 286 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: B 311 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7651 (tptp) REVERT: B 359 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7469 (mptt) REVERT: B 375 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: B 440 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8237 (mttm) REVERT: B 501 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7461 (tp) REVERT: B 533 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6712 (mtmm) REVERT: B 551 GLN cc_start: 0.6290 (mp10) cc_final: 0.5494 (pt0) REVERT: B 641 GLU cc_start: 0.4703 (mt-10) cc_final: 0.4273 (mm-30) REVERT: B 690 GLN cc_start: 0.3198 (pm20) cc_final: 0.2891 (mp10) REVERT: B 736 GLN cc_start: 0.7424 (mm-40) cc_final: 0.7038 (mm-40) REVERT: E 107 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7024 (t0) REVERT: F 84 THR cc_start: 0.7848 (m) cc_final: 0.7516 (p) REVERT: F 108 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6425 (mp) REVERT: F 122 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7521 (mtmp) REVERT: F 183 ASN cc_start: 0.6672 (p0) cc_final: 0.5869 (t0) REVERT: F 191 GLU cc_start: 0.7708 (pt0) cc_final: 0.6839 (tp30) REVERT: F 275 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8343 (t) REVERT: F 308 SER cc_start: 0.7732 (m) cc_final: 0.7389 (p) REVERT: F 375 GLU cc_start: 0.6686 (pp20) cc_final: 0.6380 (mp0) REVERT: F 429 VAL cc_start: 0.5586 (OUTLIER) cc_final: 0.5230 (t) REVERT: F 435 ASN cc_start: 0.7085 (t0) cc_final: 0.6498 (t0) REVERT: F 544 GLU cc_start: 0.5098 (OUTLIER) cc_final: 0.4551 (mm-30) REVERT: F 550 GLU cc_start: 0.4455 (OUTLIER) cc_final: 0.4039 (mt-10) REVERT: I 25 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6192 (mp0) REVERT: I 35 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6765 (ttpp) REVERT: I 66 ARG cc_start: 0.7334 (mpp80) cc_final: 0.7010 (mpt90) REVERT: I 72 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6978 (mp) REVERT: I 141 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7874 (tp) REVERT: I 151 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6961 (tm-30) REVERT: I 205 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8531 (m) REVERT: I 209 GLU cc_start: 0.7583 (tp30) cc_final: 0.7015 (mp0) REVERT: I 342 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: J 86 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6384 (mmm160) REVERT: J 91 ARG cc_start: 0.5875 (tpt170) cc_final: 0.3450 (mtp180) REVERT: J 191 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6952 (mm-30) REVERT: J 203 ARG cc_start: 0.5831 (OUTLIER) cc_final: 0.5337 (ttt180) REVERT: J 348 LYS cc_start: 0.8092 (pttp) cc_final: 0.7806 (pptt) REVERT: J 440 LYS cc_start: 0.6512 (OUTLIER) cc_final: 0.5743 (ptpp) REVERT: M 38 ASN cc_start: 0.8335 (t0) cc_final: 0.7841 (t0) REVERT: M 42 ARG cc_start: 0.7536 (mtm110) cc_final: 0.7025 (mtp180) REVERT: M 50 ILE cc_start: 0.8483 (mm) cc_final: 0.8119 (mm) REVERT: M 55 ASN cc_start: 0.7616 (t0) cc_final: 0.7285 (t0) REVERT: M 211 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8187 (mtpt) REVERT: M 288 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6304 (mmtt) REVERT: M 293 LYS cc_start: 0.6565 (OUTLIER) cc_final: 0.6175 (tptm) REVERT: M 361 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.6833 (tt) REVERT: N 91 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.5752 (tpt90) REVERT: N 122 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8244 (mtpt) REVERT: N 174 LYS cc_start: 0.7436 (mtpp) cc_final: 0.7166 (ttmt) REVERT: N 180 ASN cc_start: 0.7679 (p0) cc_final: 0.7391 (p0) REVERT: N 212 ASP cc_start: 0.7450 (m-30) cc_final: 0.6997 (m-30) REVERT: N 263 GLU cc_start: 0.7209 (tt0) cc_final: 0.6372 (mt-10) REVERT: N 398 GLU cc_start: 0.7001 (tp30) cc_final: 0.6709 (tt0) REVERT: N 440 LYS cc_start: 0.8809 (ptpp) cc_final: 0.8554 (ptmt) REVERT: N 471 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.5697 (mp0) REVERT: N 531 SER cc_start: 0.6688 (OUTLIER) cc_final: 0.6085 (p) REVERT: N 551 GLN cc_start: 0.6333 (OUTLIER) cc_final: 0.5999 (tm-30) REVERT: N 558 ASN cc_start: 0.6979 (m-40) cc_final: 0.6708 (m110) REVERT: N 680 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6135 (tppt) REVERT: N 685 PHE cc_start: 0.4899 (OUTLIER) cc_final: 0.4353 (m-80) outliers start: 164 outliers final: 98 residues processed: 462 average time/residue: 0.6102 time to fit residues: 360.4139 Evaluate side-chains 450 residues out of total 3786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 314 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 550 GLU Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 690 GLN Chi-restraints excluded: chain F residue 698 VAL Chi-restraints excluded: chain F residue 708 LYS Chi-restraints excluded: chain F residue 741 ILE Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 129 LYS Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain I residue 201 ASP Chi-restraints excluded: chain I residue 205 SER Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 170 ASN Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 203 ARG Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 439 SER Chi-restraints excluded: chain J residue 440 LYS Chi-restraints excluded: chain J residue 501 ILE Chi-restraints excluded: chain J residue 531 SER Chi-restraints excluded: chain J residue 550 GLU Chi-restraints excluded: chain J residue 648 LEU Chi-restraints excluded: chain J residue 674 GLU Chi-restraints excluded: chain J residue 691 MET Chi-restraints excluded: chain J residue 698 VAL Chi-restraints excluded: chain J residue 699 THR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 196 SER Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 251 VAL Chi-restraints excluded: chain M residue 288 LYS Chi-restraints excluded: chain M residue 293 LYS Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 27 CYS Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 122 LYS Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 410 SER Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 439 SER Chi-restraints excluded: chain N residue 451 ILE Chi-restraints excluded: chain N residue 471 GLU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 531 SER Chi-restraints excluded: chain N residue 551 GLN Chi-restraints excluded: chain N residue 553 LEU Chi-restraints excluded: chain N residue 680 LYS Chi-restraints excluded: chain N residue 685 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 439 optimal weight: 7.9990 chunk 337 optimal weight: 1.9990 chunk 431 optimal weight: 0.7980 chunk 404 optimal weight: 0.9990 chunk 434 optimal weight: 50.0000 chunk 194 optimal weight: 0.5980 chunk 245 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 400 optimal weight: 0.5980 chunk 425 optimal weight: 0.0060 chunk 103 optimal weight: 50.0000 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN E 113 ASN E 138 GLN ** F 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 GLN ** M 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN ** N 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 558 ASN N 736 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.235342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.173950 restraints weight = 50906.152| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.86 r_work: 0.3816 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43613 Z= 0.124 Angle : 0.536 10.142 60664 Z= 0.296 Chirality : 0.041 0.310 7041 Planarity : 0.004 0.070 6119 Dihedral : 22.371 176.822 10042 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.07 % Rotamer: Outliers : 3.78 % Allowed : 29.71 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.67 (0.13), residues: 3990 helix: 1.26 (0.11), residues: 2087 sheet: -0.19 (0.23), residues: 545 loop : -0.43 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 42 TYR 0.025 0.001 TYR A 150 PHE 0.032 0.001 PHE F 184 TRP 0.010 0.001 TRP B 559 HIS 0.012 0.001 HIS I 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (43613) covalent geometry : angle 0.53620 / 0.30 (60664) hydrogen bonds : bond 0.03882 / 2.52 ( 1958) hydrogen bonds : angle 4.22559 / 3.01 ( 5483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18103.61 seconds wall clock time: 308 minutes 5.19 seconds (18485.19 seconds total)