Starting phenix.real_space_refine on Sat Oct 11 22:41:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sal_40273/10_2025/8sal_40273_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sal_40273/10_2025/8sal_40273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sal_40273/10_2025/8sal_40273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sal_40273/10_2025/8sal_40273.map" model { file = "/net/cci-nas-00/data/ceres_data/8sal_40273/10_2025/8sal_40273_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sal_40273/10_2025/8sal_40273_neut.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 11596 2.51 5 N 3211 2.21 5 O 3494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18435 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3508 Classifications: {'peptide': 448} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 425} Chain breaks: 1 Chain: "B" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 904 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 2 Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "D" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Chain: "E" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3425 Classifications: {'peptide': 437} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 413} Chain breaks: 2 Chain: "F" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 900 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "H" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Chain: "I" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3503 Classifications: {'peptide': 447} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain breaks: 1 Chain: "J" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 945 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Time building chain proxies: 4.85, per 1000 atoms: 0.26 Number of scatterers: 18435 At special positions: 0 Unit cell: (143.91, 150.306, 112.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 134 16.00 O 3494 8.00 N 3211 7.00 C 11596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 165 " distance=2.02 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 187 " - pdb=" SG CYS A 216 " distance=2.04 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 379 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 44 " distance=2.03 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS E 165 " distance=2.02 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 124 " distance=2.03 Simple disulfide: pdb=" SG CYS E 187 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 197 " - pdb=" SG CYS E 208 " distance=2.03 Simple disulfide: pdb=" SG CYS E 265 " - pdb=" SG CYS E 299 " distance=2.03 Simple disulfide: pdb=" SG CYS E 345 " - pdb=" SG CYS E 406 " distance=2.03 Simple disulfide: pdb=" SG CYS E 352 " - pdb=" SG CYS E 379 " distance=2.03 Simple disulfide: pdb=" SG CYS F 562 " - pdb=" SG CYS F 568 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 44 " distance=2.02 Simple disulfide: pdb=" SG CYS I 89 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 96 " - pdb=" SG CYS I 165 " distance=2.02 Simple disulfide: pdb=" SG CYS I 101 " - pdb=" SG CYS I 124 " distance=2.03 Simple disulfide: pdb=" SG CYS I 187 " - pdb=" SG CYS I 216 " distance=2.03 Simple disulfide: pdb=" SG CYS I 197 " - pdb=" SG CYS I 208 " distance=2.03 Simple disulfide: pdb=" SG CYS I 265 " - pdb=" SG CYS I 299 " distance=2.03 Simple disulfide: pdb=" SG CYS I 345 " - pdb=" SG CYS I 406 " distance=2.03 Simple disulfide: pdb=" SG CYS I 352 " - pdb=" SG CYS I 379 " distance=2.03 Simple disulfide: pdb=" SG CYS J 562 " - pdb=" SG CYS J 568 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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: 1.60 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4322 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 48 sheets defined 22.1% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 69 through 87 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 304 through 321 removed outlier: 3.929A pdb=" N HIS A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.760A pdb=" N PHE A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'B' and resid 485 through 491 Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.759A pdb=" N MET B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 509 removed outlier: 4.585A pdb=" N GLN B 504 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 536 removed outlier: 3.777A pdb=" N GLY B 536 " --> pdb=" O THR B 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 533 through 536' Processing helix chain 'B' and resid 537 through 560 removed outlier: 4.191A pdb=" N GLN B 541 " --> pdb=" O ILE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 587 Processing helix chain 'B' and resid 591 through 601 removed outlier: 3.545A pdb=" N TRP B 595 " --> pdb=" O THR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 619 removed outlier: 3.860A pdb=" N GLN B 617 " --> pdb=" O SER B 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 removed outlier: 3.769A pdb=" N GLN C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 69 through 87 Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 164 through 167 Processing helix chain 'E' and resid 304 through 321 removed outlier: 4.001A pdb=" N HIS E 311 " --> pdb=" O ASN E 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU E 312 " --> pdb=" O LYS E 308 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.759A pdb=" N PHE E 358 " --> pdb=" O THR E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 366 Processing helix chain 'E' and resid 436 through 443 Processing helix chain 'E' and resid 444 through 446 No H-bonds generated for 'chain 'E' and resid 444 through 446' Processing helix chain 'F' and resid 486 through 491 Processing helix chain 'F' and resid 493 through 498 Processing helix chain 'F' and resid 500 through 509 removed outlier: 4.401A pdb=" N GLN F 504 " --> pdb=" O THR F 500 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA F 505 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU F 509 " --> pdb=" O ALA F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 537 Processing helix chain 'F' and resid 538 through 560 removed outlier: 3.728A pdb=" N ALA F 542 " --> pdb=" O LYS F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 588 removed outlier: 3.560A pdb=" N ILE F 586 " --> pdb=" O ASN F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 601 removed outlier: 3.501A pdb=" N TRP F 595 " --> pdb=" O THR F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 609 through 619 Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.869A pdb=" N GLN G 64 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 69 through 87 Processing helix chain 'I' and resid 92 through 96 Processing helix chain 'I' and resid 117 through 119 No H-bonds generated for 'chain 'I' and resid 117 through 119' Processing helix chain 'I' and resid 164 through 167 Processing helix chain 'I' and resid 304 through 321 removed outlier: 3.921A pdb=" N HIS I 311 " --> pdb=" O ASN I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 340 Processing helix chain 'I' and resid 354 through 359 removed outlier: 3.812A pdb=" N PHE I 358 " --> pdb=" O THR I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 366 Processing helix chain 'I' and resid 427 through 431 Processing helix chain 'I' and resid 436 through 443 Processing helix chain 'I' and resid 444 through 446 No H-bonds generated for 'chain 'I' and resid 444 through 446' Processing helix chain 'J' and resid 485 through 491 removed outlier: 3.666A pdb=" N ALA J 489 " --> pdb=" O GLY J 485 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA J 490 " --> pdb=" O PHE J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 493 through 500 removed outlier: 3.576A pdb=" N ALA J 497 " --> pdb=" O THR J 493 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET J 499 " --> pdb=" O GLY J 495 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR J 500 " --> pdb=" O ALA J 496 " (cutoff:3.500A) Processing helix chain 'J' and resid 500 through 508 removed outlier: 3.646A pdb=" N GLN J 504 " --> pdb=" O THR J 500 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN J 507 " --> pdb=" O VAL J 503 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 536 removed outlier: 3.824A pdb=" N GLY J 536 " --> pdb=" O THR J 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 533 through 536' Processing helix chain 'J' and resid 537 through 560 removed outlier: 3.729A pdb=" N GLN J 541 " --> pdb=" O ILE J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 588 Processing helix chain 'J' and resid 591 through 601 removed outlier: 3.677A pdb=" N ASN J 601 " --> pdb=" O LYS J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 610 through 618 Processing helix chain 'K' and resid 60 through 64 removed outlier: 3.971A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 3.667A pdb=" N ILE A 194 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 25 removed outlier: 3.634A pdb=" N PHE A 23 " --> pdb=" O CYS A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 64 Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 144 Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 230 removed outlier: 6.332A pdb=" N LEU A 229 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N THR A 405 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N ILE A 263 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N LYS A 407 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N VAL A 261 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N ASN A 409 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N THR A 259 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR A 411 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 228 through 230 removed outlier: 6.332A pdb=" N LEU A 229 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N THR A 405 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N ILE A 263 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N LYS A 407 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N VAL A 261 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N ASN A 409 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N THR A 259 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR A 411 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS A 299 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 377 " --> pdb=" O CYS A 299 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 272 through 277 removed outlier: 6.794A pdb=" N THR A 272 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 343 removed outlier: 3.520A pdb=" N PHE A 343 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE A 349 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 382 " --> pdb=" O PHE A 349 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 384 through 386 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.374A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 94 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.374A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 107 " --> pdb=" O TYR C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.421A pdb=" N LEU D 11 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.421A pdb=" N LEU D 11 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 15 through 16 removed outlier: 3.760A pdb=" N ILE E 194 " --> pdb=" O VAL E 214 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 23 through 25 removed outlier: 3.522A pdb=" N PHE E 23 " --> pdb=" O CYS E 187 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR E 186 " --> pdb=" O HIS E 218 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS E 218 " --> pdb=" O TYR E 186 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 61 through 64 Processing sheet with id=AC2, first strand: chain 'E' and resid 141 through 144 Processing sheet with id=AC3, first strand: chain 'E' and resid 127 through 129 Processing sheet with id=AC4, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.299A pdb=" N LEU E 229 " --> pdb=" O THR E 411 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N THR E 405 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 11.776A pdb=" N ILE E 263 " --> pdb=" O THR E 405 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N LYS E 407 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 11.102A pdb=" N VAL E 261 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N ASN E 409 " --> pdb=" O THR E 259 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N THR E 259 " --> pdb=" O ASN E 409 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR E 411 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.299A pdb=" N LEU E 229 " --> pdb=" O THR E 411 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N THR E 405 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 11.776A pdb=" N ILE E 263 " --> pdb=" O THR E 405 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N LYS E 407 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 11.102A pdb=" N VAL E 261 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N ASN E 409 " --> pdb=" O THR E 259 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N THR E 259 " --> pdb=" O ASN E 409 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR E 411 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS E 299 " --> pdb=" O LEU E 377 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 272 through 277 removed outlier: 6.814A pdb=" N THR E 272 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 341 through 343 removed outlier: 3.836A pdb=" N PHE E 349 " --> pdb=" O LYS E 382 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 385 through 386 Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'G' and resid 47 through 51 removed outlier: 6.205A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG G 94 " --> pdb=" O HIS G 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 47 through 51 removed outlier: 6.205A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.516A pdb=" N ARG H 24 " --> pdb=" O THR H 5 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.395A pdb=" N LEU H 11 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.395A pdb=" N LEU H 11 " --> pdb=" O GLN H 105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 9 through 16 removed outlier: 5.933A pdb=" N TYR I 10 " --> pdb=" O GLY I 457 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLY I 457 " --> pdb=" O TYR I 10 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL I 14 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE I 453 " --> pdb=" O VAL I 14 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS I 16 " --> pdb=" O VAL I 451 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL I 451 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE I 194 " --> pdb=" O VAL I 214 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 23 through 25 Processing sheet with id=AD8, first strand: chain 'I' and resid 61 through 64 Processing sheet with id=AD9, first strand: chain 'I' and resid 141 through 144 Processing sheet with id=AE1, first strand: chain 'I' and resid 127 through 129 Processing sheet with id=AE2, first strand: chain 'I' and resid 228 through 230 removed outlier: 6.337A pdb=" N LEU I 229 " --> pdb=" O THR I 411 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N THR I 405 " --> pdb=" O ILE I 263 " (cutoff:3.500A) removed outlier: 11.758A pdb=" N ILE I 263 " --> pdb=" O THR I 405 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N LYS I 407 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 11.111A pdb=" N VAL I 261 " --> pdb=" O LYS I 407 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N ASN I 409 " --> pdb=" O THR I 259 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N THR I 259 " --> pdb=" O ASN I 409 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR I 411 " --> pdb=" O LEU I 257 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 228 through 230 removed outlier: 6.337A pdb=" N LEU I 229 " --> pdb=" O THR I 411 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N THR I 405 " --> pdb=" O ILE I 263 " (cutoff:3.500A) removed outlier: 11.758A pdb=" N ILE I 263 " --> pdb=" O THR I 405 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N LYS I 407 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 11.111A pdb=" N VAL I 261 " --> pdb=" O LYS I 407 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N ASN I 409 " --> pdb=" O THR I 259 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N THR I 259 " --> pdb=" O ASN I 409 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR I 411 " --> pdb=" O LEU I 257 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS I 299 " --> pdb=" O LEU I 377 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 272 through 277 removed outlier: 6.738A pdb=" N THR I 272 " --> pdb=" O GLY I 288 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 341 through 343 removed outlier: 4.041A pdb=" N PHE I 349 " --> pdb=" O LYS I 382 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS I 382 " --> pdb=" O PHE I 349 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 384 through 386 Processing sheet with id=AE7, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'K' and resid 46 through 51 removed outlier: 6.421A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG K 94 " --> pdb=" O HIS K 102 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 46 through 51 removed outlier: 6.421A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR K 107 " --> pdb=" O TYR K 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.399A pdb=" N LEU L 11 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.399A pdb=" N LEU L 11 " --> pdb=" O GLN L 105 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 6478 1.37 - 1.53: 10551 1.53 - 1.69: 1630 1.69 - 1.84: 179 1.84 - 2.00: 3 Bond restraints: 18841 Sorted by residual: bond pdb=" CB CYS F 569 " pdb=" SG CYS F 569 " ideal model delta sigma weight residual 1.808 1.998 -0.190 3.30e-02 9.18e+02 3.30e+01 bond pdb=" CB CYS B 569 " pdb=" SG CYS B 569 " ideal model delta sigma weight residual 1.808 1.995 -0.187 3.30e-02 9.18e+02 3.21e+01 bond pdb=" CB CYS J 569 " pdb=" SG CYS J 569 " ideal model delta sigma weight residual 1.808 1.990 -0.182 3.30e-02 9.18e+02 3.04e+01 bond pdb=" C ASP I 48 " pdb=" N PRO I 49 " ideal model delta sigma weight residual 1.331 1.362 -0.030 7.90e-03 1.60e+04 1.45e+01 bond pdb=" C VAL A 458 " pdb=" N ALA A 459 " ideal model delta sigma weight residual 1.329 1.364 -0.035 1.40e-02 5.10e+03 6.31e+00 ... (remaining 18836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 25096 2.85 - 5.69: 429 5.69 - 8.54: 41 8.54 - 11.39: 3 11.39 - 14.23: 1 Bond angle restraints: 25570 Sorted by residual: angle pdb=" CA CYS F 569 " pdb=" CB CYS F 569 " pdb=" SG CYS F 569 " ideal model delta sigma weight residual 114.40 128.63 -14.23 2.30e+00 1.89e-01 3.83e+01 angle pdb=" N THR J 570 " pdb=" CA THR J 570 " pdb=" C THR J 570 " ideal model delta sigma weight residual 112.89 119.91 -7.02 1.24e+00 6.50e-01 3.20e+01 angle pdb=" N THR B 570 " pdb=" CA THR B 570 " pdb=" C THR B 570 " ideal model delta sigma weight residual 112.68 119.33 -6.65 1.33e+00 5.65e-01 2.50e+01 angle pdb=" N LEU F 609 " pdb=" CA LEU F 609 " pdb=" C LEU F 609 " ideal model delta sigma weight residual 111.71 117.17 -5.46 1.15e+00 7.56e-01 2.26e+01 angle pdb=" N LYS A 422 " pdb=" CA LYS A 422 " pdb=" C LYS A 422 " ideal model delta sigma weight residual 108.34 100.64 7.70 1.64e+00 3.72e-01 2.21e+01 ... (remaining 25565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10284 17.97 - 35.94: 830 35.94 - 53.91: 141 53.91 - 71.88: 29 71.88 - 89.85: 21 Dihedral angle restraints: 11305 sinusoidal: 4567 harmonic: 6738 Sorted by residual: dihedral pdb=" CA THR I 421 " pdb=" C THR I 421 " pdb=" N LYS I 422 " pdb=" CA LYS I 422 " ideal model delta harmonic sigma weight residual 180.00 131.22 48.78 0 5.00e+00 4.00e-02 9.52e+01 dihedral pdb=" CA THR A 421 " pdb=" C THR A 421 " pdb=" N LYS A 422 " pdb=" CA LYS A 422 " ideal model delta harmonic sigma weight residual 180.00 134.26 45.74 0 5.00e+00 4.00e-02 8.37e+01 dihedral pdb=" CA LYS A 33 " pdb=" C LYS A 33 " pdb=" N GLU A 34 " pdb=" CA GLU A 34 " ideal model delta harmonic sigma weight residual 180.00 140.25 39.75 0 5.00e+00 4.00e-02 6.32e+01 ... (remaining 11302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2165 0.049 - 0.099: 434 0.099 - 0.148: 196 0.148 - 0.197: 18 0.197 - 0.246: 1 Chirality restraints: 2814 Sorted by residual: chirality pdb=" CG LEU A 4 " pdb=" CB LEU A 4 " pdb=" CD1 LEU A 4 " pdb=" CD2 LEU A 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE B 567 " pdb=" N ILE B 567 " pdb=" C ILE B 567 " pdb=" CB ILE B 567 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA ILE J 567 " pdb=" N ILE J 567 " pdb=" C ILE J 567 " pdb=" CB ILE J 567 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 2811 not shown) Planarity restraints: 3281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 9 " -0.037 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR I 9 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR I 9 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR I 9 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR I 9 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR I 9 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR I 9 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR I 9 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 459 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ALA E 459 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA E 459 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO E 460 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 459 " -0.047 5.00e-02 4.00e+02 7.35e-02 8.63e+00 pdb=" N PRO E 460 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO E 460 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 460 " -0.040 5.00e-02 4.00e+02 ... (remaining 3278 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 281 2.63 - 3.20: 17579 3.20 - 3.77: 28336 3.77 - 4.33: 38450 4.33 - 4.90: 62494 Nonbonded interactions: 147140 Sorted by model distance: nonbonded pdb=" OG1 THR A 416 " pdb=" O GLU A 428 " model vdw 2.065 3.040 nonbonded pdb=" OE1 GLU I 303 " pdb=" OG SER I 371 " model vdw 2.096 3.040 nonbonded pdb=" OE1 GLU E 303 " pdb=" OG SER E 371 " model vdw 2.097 3.040 nonbonded pdb=" OE1 GLU A 303 " pdb=" OG SER A 371 " model vdw 2.098 3.040 nonbonded pdb=" O ASN E 440 " pdb=" OG SER E 443 " model vdw 2.111 3.040 ... (remaining 147135 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' and (resid 3 through 418 or resid 431 through 458)) selection = (chain 'E' and resid 3 through 458) selection = (chain 'I' and (resid 3 through 418 or resid 431 through 458)) } ncs_group { reference = (chain 'B' and (resid 485 through 510 or resid 533 through 619)) selection = (chain 'F' and (resid 485 through 561 or resid 567 through 619)) selection = (chain 'J' and (resid 485 through 510 or resid 533 through 561 or resid 567 thro \ ugh 619)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.370 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.480 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.190 18879 Z= 0.229 Angle : 0.892 14.235 25646 Z= 0.499 Chirality : 0.049 0.246 2814 Planarity : 0.005 0.073 3281 Dihedral : 13.673 89.852 6869 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.45 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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 aren not related in a simple way. whole: -2.31 (0.17), residues: 2297 helix: -0.35 (0.26), residues: 392 sheet: -1.58 (0.19), residues: 611 loop : -1.90 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 442 TYR 0.063 0.002 TYR I 9 PHE 0.019 0.002 PHE K 100D TRP 0.046 0.002 TRP J 560 HIS 0.010 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00502 (18841) covalent geometry : angle 0.88946 (25570) SS BOND : bond 0.00327 ( 38) SS BOND : angle 1.61142 ( 76) hydrogen bonds : bond 0.23008 ( 597) hydrogen bonds : angle 8.94198 ( 1623) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 678 time to evaluate : 0.610 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8400 (t80) cc_final: 0.7355 (p90) REVERT: A 16 LYS cc_start: 0.9238 (mmtm) cc_final: 0.9027 (mmmm) REVERT: A 65 MET cc_start: 0.9072 (ppp) cc_final: 0.8822 (ppp) REVERT: A 70 MET cc_start: 0.9703 (ppp) cc_final: 0.9447 (ppp) REVERT: A 74 MET cc_start: 0.9620 (tmm) cc_final: 0.9276 (tmm) REVERT: A 83 ASP cc_start: 0.9733 (t70) cc_final: 0.9527 (t0) REVERT: A 121 MET cc_start: 0.9568 (tpp) cc_final: 0.9256 (tpp) REVERT: A 249 ASN cc_start: 0.9218 (p0) cc_final: 0.8739 (p0) REVERT: A 338 ILE cc_start: 0.9406 (mm) cc_final: 0.9139 (mt) REVERT: A 350 PHE cc_start: 0.9240 (m-80) cc_final: 0.8475 (m-80) REVERT: A 357 LEU cc_start: 0.9647 (mt) cc_final: 0.9415 (mt) REVERT: A 358 PHE cc_start: 0.9391 (m-80) cc_final: 0.9045 (m-80) REVERT: A 377 LEU cc_start: 0.9621 (mt) cc_final: 0.9051 (tp) REVERT: A 395 MET cc_start: 0.9356 (ppp) cc_final: 0.9062 (ppp) REVERT: A 415 LEU cc_start: 0.9351 (mt) cc_final: 0.9085 (tp) REVERT: A 437 MET cc_start: 0.8984 (tpt) cc_final: 0.7895 (tpt) REVERT: A 454 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8302 (mp0) REVERT: B 587 TRP cc_start: 0.8958 (m100) cc_final: 0.8663 (m100) REVERT: B 599 ILE cc_start: 0.9529 (pt) cc_final: 0.8810 (pt) REVERT: B 607 TYR cc_start: 0.8406 (m-10) cc_final: 0.8144 (m-10) REVERT: C 4 LEU cc_start: 0.9354 (mt) cc_final: 0.8668 (mp) REVERT: C 36 TRP cc_start: 0.9280 (m100) cc_final: 0.8899 (m-10) REVERT: C 48 MET cc_start: 0.9403 (mmp) cc_final: 0.9115 (mmm) REVERT: C 73 VAL cc_start: 0.8327 (m) cc_final: 0.8057 (p) REVERT: C 80 LEU cc_start: 0.9764 (tp) cc_final: 0.9312 (tp) REVERT: C 97 ASN cc_start: 0.8662 (t0) cc_final: 0.8212 (p0) REVERT: D 60 ASP cc_start: 0.9513 (p0) cc_final: 0.9300 (t0) REVERT: D 87 TYR cc_start: 0.9233 (m-80) cc_final: 0.8939 (m-80) REVERT: E 22 LEU cc_start: 0.9703 (mt) cc_final: 0.9431 (tp) REVERT: E 70 MET cc_start: 0.9631 (ppp) cc_final: 0.9210 (ppp) REVERT: E 78 ILE cc_start: 0.9551 (mt) cc_final: 0.9263 (tp) REVERT: E 82 TRP cc_start: 0.9107 (t60) cc_final: 0.8866 (t60) REVERT: E 121 MET cc_start: 0.8996 (mmp) cc_final: 0.8607 (tpp) REVERT: E 156 ASN cc_start: 0.9122 (t0) cc_final: 0.8823 (p0) REVERT: E 298 HIS cc_start: 0.8823 (m-70) cc_final: 0.8330 (m-70) REVERT: E 306 TRP cc_start: 0.9714 (t-100) cc_final: 0.9497 (t-100) REVERT: E 343 PHE cc_start: 0.9129 (p90) cc_final: 0.7919 (p90) REVERT: E 350 PHE cc_start: 0.9258 (m-80) cc_final: 0.8278 (m-80) REVERT: E 351 TYR cc_start: 0.9228 (m-80) cc_final: 0.8845 (m-80) REVERT: E 385 ILE cc_start: 0.9281 (tp) cc_final: 0.8985 (tp) REVERT: E 395 MET cc_start: 0.9367 (ppp) cc_final: 0.8731 (ppp) REVERT: E 414 LEU cc_start: 0.9778 (mt) cc_final: 0.9481 (mt) REVERT: E 437 MET cc_start: 0.9227 (mmt) cc_final: 0.8372 (tpp) REVERT: E 441 TRP cc_start: 0.9352 (m-10) cc_final: 0.8732 (m-90) REVERT: F 544 VAL cc_start: 0.9823 (t) cc_final: 0.9559 (p) REVERT: F 565 LYS cc_start: 0.9424 (mmtp) cc_final: 0.9139 (ptpp) REVERT: F 599 ILE cc_start: 0.9476 (pt) cc_final: 0.8923 (pt) REVERT: G 27 TYR cc_start: 0.6920 (t80) cc_final: 0.6433 (t80) REVERT: G 28 GLU cc_start: 0.9748 (mp0) cc_final: 0.9278 (tp30) REVERT: G 69 MET cc_start: 0.8968 (pmm) cc_final: 0.8761 (pmm) REVERT: G 82 LEU cc_start: 0.9384 (tt) cc_final: 0.9145 (tp) REVERT: G 97 ASN cc_start: 0.8802 (t0) cc_final: 0.8258 (p0) REVERT: H 54 ARG cc_start: 0.8510 (mpt180) cc_final: 0.8257 (mtt90) REVERT: H 87 TYR cc_start: 0.9343 (m-80) cc_final: 0.8979 (m-80) REVERT: I 65 MET cc_start: 0.9285 (ppp) cc_final: 0.8589 (ppp) REVERT: I 68 ASN cc_start: 0.9173 (t0) cc_final: 0.8743 (t0) REVERT: I 83 ASP cc_start: 0.9717 (t0) cc_final: 0.9514 (t0) REVERT: I 121 MET cc_start: 0.9671 (tpp) cc_final: 0.9292 (tpp) REVERT: I 156 ASN cc_start: 0.9149 (t0) cc_final: 0.8802 (p0) REVERT: I 249 ASN cc_start: 0.9150 (p0) cc_final: 0.8713 (p0) REVERT: I 298 HIS cc_start: 0.8913 (m-70) cc_final: 0.8398 (m-70) REVERT: I 306 TRP cc_start: 0.9787 (t-100) cc_final: 0.9538 (t-100) REVERT: I 328 TYR cc_start: 0.8870 (m-80) cc_final: 0.8604 (m-80) REVERT: I 343 PHE cc_start: 0.8935 (p90) cc_final: 0.7866 (p90) REVERT: I 350 PHE cc_start: 0.9231 (m-80) cc_final: 0.8373 (m-80) REVERT: I 385 ILE cc_start: 0.9349 (tp) cc_final: 0.8876 (pt) REVERT: I 395 MET cc_start: 0.9488 (ppp) cc_final: 0.8959 (ppp) REVERT: I 400 ILE cc_start: 0.9320 (mt) cc_final: 0.8818 (pt) REVERT: I 414 LEU cc_start: 0.9507 (mt) cc_final: 0.8909 (mt) REVERT: I 415 LEU cc_start: 0.9363 (mt) cc_final: 0.9023 (tp) REVERT: I 437 MET cc_start: 0.9191 (mmp) cc_final: 0.8167 (tpt) REVERT: J 547 VAL cc_start: 0.9659 (t) cc_final: 0.9304 (p) REVERT: J 599 ILE cc_start: 0.9559 (pt) cc_final: 0.8987 (pt) REVERT: K 4 LEU cc_start: 0.9235 (mt) cc_final: 0.8688 (mp) REVERT: K 23 ARG cc_start: 0.9136 (ttm110) cc_final: 0.8916 (ptp90) REVERT: K 27 TYR cc_start: 0.7012 (t80) cc_final: 0.6423 (t80) REVERT: K 28 GLU cc_start: 0.9758 (mp0) cc_final: 0.9206 (tp30) REVERT: K 48 MET cc_start: 0.9364 (mmp) cc_final: 0.9161 (mmm) REVERT: K 82 LEU cc_start: 0.9429 (tt) cc_final: 0.9025 (tp) REVERT: K 97 ASN cc_start: 0.8635 (t0) cc_final: 0.8305 (p0) REVERT: L 87 TYR cc_start: 0.9199 (m-80) cc_final: 0.8896 (m-80) outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.1578 time to fit residues: 154.1369 Evaluate side-chains 437 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 42 HIS ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 318 GLN A 423 ASN B 604 GLN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 90 GLN E 3 ASN E 75 HIS E 127 ASN E 271 ASN E 298 HIS E 305 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 ASN I 305 GLN I 423 ASN ** I 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 89 GLN L 90 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.043046 restraints weight = 141437.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.044679 restraints weight = 89893.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.045867 restraints weight = 63705.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.046808 restraints weight = 48785.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.047540 restraints weight = 38904.241| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 18879 Z= 0.295 Angle : 0.890 11.450 25646 Z= 0.482 Chirality : 0.050 0.171 2814 Planarity : 0.006 0.061 3281 Dihedral : 7.559 37.766 2530 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.97 % Favored : 91.90 % Rotamer: Outliers : 0.64 % Allowed : 5.59 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -2.29 (0.16), residues: 2297 helix: -0.87 (0.23), residues: 416 sheet: -1.59 (0.21), residues: 569 loop : -1.70 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 267 TYR 0.047 0.003 TYR C 100 PHE 0.037 0.004 PHE A 179 TRP 0.051 0.004 TRP A 441 HIS 0.009 0.002 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00624 (18841) covalent geometry : angle 0.88654 (25570) SS BOND : bond 0.00489 ( 38) SS BOND : angle 1.60173 ( 76) hydrogen bonds : bond 0.05230 ( 597) hydrogen bonds : angle 6.93876 ( 1623) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 425 time to evaluate : 0.528 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: 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: 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: 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: symmetry clash REVERT: A 15 TRP cc_start: 0.8667 (m-90) cc_final: 0.8395 (m-90) REVERT: A 36 HIS cc_start: 0.7880 (m-70) cc_final: 0.7564 (m170) REVERT: A 65 MET cc_start: 0.9571 (ppp) cc_final: 0.9044 (ppp) REVERT: A 66 TRP cc_start: 0.9183 (m100) cc_final: 0.8896 (m100) REVERT: A 143 PHE cc_start: 0.9767 (m-10) cc_final: 0.9551 (m-80) REVERT: A 162 LEU cc_start: 0.9598 (mt) cc_final: 0.9321 (mt) REVERT: A 246 LEU cc_start: 0.9633 (mt) cc_final: 0.9360 (pt) REVERT: A 251 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8269 (mmtm) REVERT: A 388 TRP cc_start: 0.8317 (t60) cc_final: 0.8069 (t-100) REVERT: A 389 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 395 MET cc_start: 0.9586 (ppp) cc_final: 0.9285 (ppp) REVERT: A 415 LEU cc_start: 0.9568 (mt) cc_final: 0.9292 (tp) REVERT: A 454 GLU cc_start: 0.8704 (mm-30) cc_final: 0.7828 (mp0) REVERT: B 494 MET cc_start: 0.8376 (ttt) cc_final: 0.7533 (mmm) REVERT: B 548 GLU cc_start: 0.9543 (tt0) cc_final: 0.9284 (tt0) REVERT: B 549 ARG cc_start: 0.9665 (mtp180) cc_final: 0.9316 (mmm-85) REVERT: B 554 GLN cc_start: 0.9348 (mm-40) cc_final: 0.9120 (mm110) REVERT: B 560 TRP cc_start: 0.8826 (m-90) cc_final: 0.7388 (m-90) REVERT: B 614 GLN cc_start: 0.9612 (tp40) cc_final: 0.9395 (tm-30) REVERT: B 618 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8334 (tm-30) REVERT: C 27 TYR cc_start: 0.7021 (t80) cc_final: 0.6589 (t80) REVERT: C 37 ILE cc_start: 0.9717 (tt) cc_final: 0.9370 (mm) REVERT: C 97 ASN cc_start: 0.9278 (t0) cc_final: 0.8892 (p0) REVERT: C 100 TYR cc_start: 0.8961 (m-80) cc_final: 0.8630 (t80) REVERT: D 38 GLN cc_start: 0.9679 (OUTLIER) cc_final: 0.9445 (pp30) REVERT: D 87 TYR cc_start: 0.9339 (m-80) cc_final: 0.8866 (m-80) REVERT: E 9 TYR cc_start: 0.8418 (m-10) cc_final: 0.7531 (m-80) REVERT: E 15 TRP cc_start: 0.8664 (m-90) cc_final: 0.8169 (m-90) REVERT: E 65 MET cc_start: 0.9450 (ppp) cc_final: 0.9011 (ppp) REVERT: E 68 ASN cc_start: 0.9168 (t0) cc_final: 0.8640 (t0) REVERT: E 74 MET cc_start: 0.9599 (ppp) cc_final: 0.9302 (ppp) REVERT: E 76 GLU cc_start: 0.9666 (mm-30) cc_final: 0.9363 (mm-30) REVERT: E 118 MET cc_start: 0.8571 (mmp) cc_final: 0.8349 (mmp) REVERT: E 156 ASN cc_start: 0.9147 (t0) cc_final: 0.8860 (p0) REVERT: E 162 LEU cc_start: 0.9364 (mt) cc_final: 0.9159 (tp) REVERT: E 164 ASN cc_start: 0.9277 (m-40) cc_final: 0.9007 (m-40) REVERT: E 306 TRP cc_start: 0.9738 (t-100) cc_final: 0.9288 (t-100) REVERT: E 350 PHE cc_start: 0.9158 (m-80) cc_final: 0.8758 (m-80) REVERT: E 395 MET cc_start: 0.9509 (ppp) cc_final: 0.9062 (ppp) REVERT: E 437 MET cc_start: 0.9382 (mmt) cc_final: 0.8687 (tpt) REVERT: E 440 ASN cc_start: 0.9563 (m110) cc_final: 0.9341 (m-40) REVERT: E 441 TRP cc_start: 0.9361 (m-10) cc_final: 0.8651 (m-90) REVERT: F 555 GLN cc_start: 0.9546 (tp40) cc_final: 0.9273 (tm-30) REVERT: F 556 LEU cc_start: 0.9741 (tp) cc_final: 0.9522 (tp) REVERT: F 559 ILE cc_start: 0.9074 (mt) cc_final: 0.8641 (mt) REVERT: G 27 TYR cc_start: 0.7538 (t80) cc_final: 0.6582 (t80) REVERT: G 28 GLU cc_start: 0.9731 (mp0) cc_final: 0.9385 (pm20) REVERT: G 52 LYS cc_start: 0.9739 (mmmt) cc_final: 0.9468 (mmtm) REVERT: G 97 ASN cc_start: 0.9319 (t0) cc_final: 0.8690 (p0) REVERT: H 36 TYR cc_start: 0.9160 (m-80) cc_final: 0.8268 (m-80) REVERT: H 87 TYR cc_start: 0.9482 (m-80) cc_final: 0.8860 (m-80) REVERT: I 65 MET cc_start: 0.9520 (ppp) cc_final: 0.9043 (ppp) REVERT: I 76 GLU cc_start: 0.9697 (mm-30) cc_final: 0.9436 (mm-30) REVERT: I 162 LEU cc_start: 0.9552 (mt) cc_final: 0.9249 (tp) REVERT: I 164 ASN cc_start: 0.9285 (m-40) cc_final: 0.8881 (m-40) REVERT: I 251 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8310 (mmmm) REVERT: I 298 HIS cc_start: 0.8626 (m-70) cc_final: 0.8234 (m90) REVERT: I 306 TRP cc_start: 0.9762 (t-100) cc_final: 0.9368 (t-100) REVERT: I 328 TYR cc_start: 0.9147 (m-80) cc_final: 0.8867 (m-80) REVERT: I 350 PHE cc_start: 0.8948 (m-80) cc_final: 0.8689 (m-80) REVERT: I 395 MET cc_start: 0.9541 (ppp) cc_final: 0.9125 (ppp) REVERT: I 415 LEU cc_start: 0.9610 (mt) cc_final: 0.9240 (tp) REVERT: I 437 MET cc_start: 0.8836 (mmp) cc_final: 0.8352 (tpt) REVERT: I 441 TRP cc_start: 0.9285 (m-90) cc_final: 0.8655 (m-90) REVERT: J 545 LEU cc_start: 0.9800 (mm) cc_final: 0.9589 (mm) REVERT: J 548 GLU cc_start: 0.9604 (tt0) cc_final: 0.9297 (mt-10) REVERT: J 554 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8971 (mm110) REVERT: K 27 TYR cc_start: 0.7442 (t80) cc_final: 0.6338 (t80) REVERT: K 28 GLU cc_start: 0.9727 (mp0) cc_final: 0.9357 (pm20) REVERT: K 80 LEU cc_start: 0.9753 (tp) cc_final: 0.9485 (tp) REVERT: K 97 ASN cc_start: 0.9095 (t0) cc_final: 0.8683 (p0) REVERT: L 87 TYR cc_start: 0.9314 (m-80) cc_final: 0.8981 (m-80) outliers start: 13 outliers final: 0 residues processed: 437 average time/residue: 0.1494 time to fit residues: 96.9301 Evaluate side-chains 325 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 140 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 23 optimal weight: 0.0770 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 HIS A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 409 ASN B 601 ASN C 64 GLN D 90 GLN E 42 HIS E 127 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN E 305 GLN E 353 ASN E 409 ASN G 64 GLN H 38 GLN I 73 GLN I 75 HIS ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 271 ASN I 320 HIS I 344 ASN K 64 GLN L 38 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.055812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.045093 restraints weight = 135904.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.046825 restraints weight = 86208.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.048101 restraints weight = 61097.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.049087 restraints weight = 46589.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.049845 restraints weight = 37206.941| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18879 Z= 0.127 Angle : 0.708 9.737 25646 Z= 0.376 Chirality : 0.047 0.216 2814 Planarity : 0.005 0.071 3281 Dihedral : 6.658 37.304 2530 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.14 % Favored : 93.73 % Rotamer: Outliers : 0.15 % Allowed : 3.48 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 aren not related in a simple way. whole: -1.87 (0.17), residues: 2297 helix: -0.30 (0.25), residues: 415 sheet: -1.22 (0.21), residues: 613 loop : -1.56 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 277 TYR 0.035 0.002 TYR L 36 PHE 0.034 0.002 PHE I 430 TRP 0.030 0.002 TRP B 560 HIS 0.004 0.001 HIS I 320 Details of bonding type rmsd covalent geometry : bond 0.00276 (18841) covalent geometry : angle 0.70462 (25570) SS BOND : bond 0.00331 ( 38) SS BOND : angle 1.39518 ( 76) hydrogen bonds : bond 0.03855 ( 597) hydrogen bonds : angle 5.96579 ( 1623) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 453 time to evaluate : 0.812 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: 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: 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: 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 10 TYR cc_start: 0.8902 (t80) cc_final: 0.7404 (p90) REVERT: A 36 HIS cc_start: 0.7618 (m-70) cc_final: 0.7309 (m170) REVERT: A 65 MET cc_start: 0.9656 (ppp) cc_final: 0.9147 (ppp) REVERT: A 121 MET cc_start: 0.9006 (mmp) cc_final: 0.8591 (tpp) REVERT: A 162 LEU cc_start: 0.9467 (mt) cc_final: 0.9199 (mt) REVERT: A 246 LEU cc_start: 0.9576 (mt) cc_final: 0.9340 (pt) REVERT: A 251 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7653 (mmtm) REVERT: A 388 TRP cc_start: 0.8282 (t60) cc_final: 0.7154 (t-100) REVERT: A 389 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8383 (pp30) REVERT: A 395 MET cc_start: 0.9605 (ppp) cc_final: 0.9347 (ppp) REVERT: A 414 LEU cc_start: 0.9571 (mt) cc_final: 0.9359 (mt) REVERT: A 415 LEU cc_start: 0.9557 (mt) cc_final: 0.9279 (tp) REVERT: A 440 ASN cc_start: 0.9460 (p0) cc_final: 0.9181 (p0) REVERT: B 494 MET cc_start: 0.8219 (ttt) cc_final: 0.7420 (mpp) REVERT: B 549 ARG cc_start: 0.9683 (mtp180) cc_final: 0.9402 (mtp180) REVERT: B 560 TRP cc_start: 0.8340 (m-10) cc_final: 0.7363 (m-90) REVERT: B 587 TRP cc_start: 0.8850 (m100) cc_final: 0.8581 (m100) REVERT: B 599 ILE cc_start: 0.9418 (pt) cc_final: 0.8952 (pt) REVERT: B 607 TYR cc_start: 0.8608 (m-80) cc_final: 0.8199 (m-80) REVERT: C 11 MET cc_start: 0.9523 (mmp) cc_final: 0.9276 (mmp) REVERT: C 27 TYR cc_start: 0.7424 (t80) cc_final: 0.5566 (t80) REVERT: C 28 GLU cc_start: 0.9054 (pm20) cc_final: 0.8551 (pm20) REVERT: C 48 MET cc_start: 0.9371 (mmp) cc_final: 0.9017 (mmm) REVERT: C 82 LEU cc_start: 0.9184 (tp) cc_final: 0.8930 (tp) REVERT: C 97 ASN cc_start: 0.9407 (t0) cc_final: 0.9066 (p0) REVERT: C 101 GLU cc_start: 0.9472 (tp30) cc_final: 0.9256 (tt0) REVERT: D 87 TYR cc_start: 0.9371 (m-80) cc_final: 0.8972 (m-80) REVERT: E 9 TYR cc_start: 0.8520 (m-10) cc_final: 0.7642 (m-80) REVERT: E 15 TRP cc_start: 0.8420 (m-90) cc_final: 0.7890 (m-90) REVERT: E 65 MET cc_start: 0.9287 (ppp) cc_final: 0.8832 (ppp) REVERT: E 74 MET cc_start: 0.9626 (ppp) cc_final: 0.9400 (ppp) REVERT: E 156 ASN cc_start: 0.9134 (t0) cc_final: 0.8876 (p0) REVERT: E 350 PHE cc_start: 0.9224 (m-80) cc_final: 0.8863 (m-80) REVERT: E 395 MET cc_start: 0.9575 (ppp) cc_final: 0.9200 (ppp) REVERT: E 437 MET cc_start: 0.9333 (mmt) cc_final: 0.9083 (tpt) REVERT: F 560 TRP cc_start: 0.9152 (m-10) cc_final: 0.8281 (m-90) REVERT: F 565 LYS cc_start: 0.9555 (mmtp) cc_final: 0.9297 (ptpp) REVERT: F 566 LEU cc_start: 0.9318 (mt) cc_final: 0.8947 (tt) REVERT: F 587 TRP cc_start: 0.8850 (m100) cc_final: 0.8378 (m100) REVERT: G 11 MET cc_start: 0.9400 (mmp) cc_final: 0.9165 (mmp) REVERT: G 27 TYR cc_start: 0.7995 (t80) cc_final: 0.7508 (t80) REVERT: G 28 GLU cc_start: 0.9764 (mp0) cc_final: 0.9475 (tp30) REVERT: G 51 LEU cc_start: 0.9497 (tp) cc_final: 0.9156 (tp) REVERT: G 82 LEU cc_start: 0.9438 (tp) cc_final: 0.9208 (tp) REVERT: G 101 GLU cc_start: 0.9442 (tp30) cc_final: 0.9161 (tt0) REVERT: H 33 LEU cc_start: 0.7759 (mm) cc_final: 0.7557 (mt) REVERT: H 87 TYR cc_start: 0.9413 (m-80) cc_final: 0.9105 (m-80) REVERT: I 65 MET cc_start: 0.9439 (ppp) cc_final: 0.9142 (ppp) REVERT: I 121 MET cc_start: 0.9589 (tpt) cc_final: 0.9176 (tpp) REVERT: I 156 ASN cc_start: 0.9107 (t0) cc_final: 0.8871 (p0) REVERT: I 162 LEU cc_start: 0.9427 (mt) cc_final: 0.9206 (mt) REVERT: I 328 TYR cc_start: 0.9240 (m-80) cc_final: 0.8924 (m-80) REVERT: I 350 PHE cc_start: 0.9072 (m-80) cc_final: 0.8770 (m-80) REVERT: I 395 MET cc_start: 0.9534 (ppp) cc_final: 0.9136 (ppp) REVERT: I 400 ILE cc_start: 0.9443 (mt) cc_final: 0.9243 (pt) REVERT: I 454 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8389 (mp0) REVERT: J 544 VAL cc_start: 0.9855 (p) cc_final: 0.9478 (p) REVERT: J 548 GLU cc_start: 0.9586 (tt0) cc_final: 0.9095 (mt-10) REVERT: J 549 ARG cc_start: 0.9596 (mmt90) cc_final: 0.9214 (mmm160) REVERT: J 551 LEU cc_start: 0.9783 (mt) cc_final: 0.9516 (pp) REVERT: J 606 ILE cc_start: 0.8145 (pt) cc_final: 0.7932 (pt) REVERT: K 27 TYR cc_start: 0.7296 (t80) cc_final: 0.7042 (t80) REVERT: K 48 MET cc_start: 0.9215 (mmt) cc_final: 0.8997 (mmm) REVERT: K 80 LEU cc_start: 0.9709 (tp) cc_final: 0.9385 (tp) REVERT: K 97 ASN cc_start: 0.9347 (t0) cc_final: 0.9018 (p0) REVERT: L 87 TYR cc_start: 0.9347 (m-80) cc_final: 0.8966 (m-80) REVERT: L 89 GLN cc_start: 0.8499 (pp30) cc_final: 0.7959 (pm20) outliers start: 3 outliers final: 0 residues processed: 456 average time/residue: 0.1467 time to fit residues: 100.4530 Evaluate side-chains 340 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 19 optimal weight: 6.9990 chunk 103 optimal weight: 0.0040 chunk 129 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 212 optimal weight: 0.0270 chunk 66 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 overall best weight: 1.9854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN D 42 GLN E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 ASN E 353 ASN E 440 ASN G 64 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 ASN ** I 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 89 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.054607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.043996 restraints weight = 138703.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.045723 restraints weight = 87759.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.047000 restraints weight = 62117.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.047994 restraints weight = 47045.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.048725 restraints weight = 37530.934| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18879 Z= 0.141 Angle : 0.686 7.268 25646 Z= 0.367 Chirality : 0.045 0.212 2814 Planarity : 0.006 0.129 3281 Dihedral : 6.417 35.438 2530 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.70 % Favored : 93.16 % Rotamer: Outliers : 0.20 % Allowed : 3.78 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -1.78 (0.17), residues: 2297 helix: -0.31 (0.25), residues: 406 sheet: -1.05 (0.21), residues: 606 loop : -1.54 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 277 TYR 0.029 0.002 TYR G 100 PHE 0.023 0.002 PHE I 430 TRP 0.025 0.002 TRP B 560 HIS 0.005 0.001 HIS K 102 Details of bonding type rmsd covalent geometry : bond 0.00310 (18841) covalent geometry : angle 0.68235 (25570) SS BOND : bond 0.00291 ( 38) SS BOND : angle 1.49935 ( 76) hydrogen bonds : bond 0.03653 ( 597) hydrogen bonds : angle 5.75941 ( 1623) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 402 time to evaluate : 0.842 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: 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: 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: 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 10 TYR cc_start: 0.9199 (t80) cc_final: 0.7681 (p90) REVERT: A 36 HIS cc_start: 0.7660 (m-70) cc_final: 0.7343 (m170) REVERT: A 65 MET cc_start: 0.9683 (ppp) cc_final: 0.9248 (ppp) REVERT: A 66 TRP cc_start: 0.9387 (m100) cc_final: 0.9050 (m100) REVERT: A 76 GLU cc_start: 0.9571 (mm-30) cc_final: 0.9341 (mm-30) REVERT: A 121 MET cc_start: 0.9063 (mmp) cc_final: 0.8615 (tpp) REVERT: A 246 LEU cc_start: 0.9593 (mt) cc_final: 0.9265 (pt) REVERT: A 251 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8401 (mmtm) REVERT: A 388 TRP cc_start: 0.8380 (t60) cc_final: 0.7719 (t-100) REVERT: A 389 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 395 MET cc_start: 0.9555 (ppp) cc_final: 0.9252 (ppp) REVERT: A 415 LEU cc_start: 0.9576 (mt) cc_final: 0.9329 (tp) REVERT: B 548 GLU cc_start: 0.9419 (tt0) cc_final: 0.9195 (tt0) REVERT: B 556 LEU cc_start: 0.9734 (tp) cc_final: 0.9460 (tp) REVERT: B 560 TRP cc_start: 0.8382 (m-10) cc_final: 0.7785 (m-90) REVERT: B 587 TRP cc_start: 0.8971 (m100) cc_final: 0.8714 (m100) REVERT: B 614 GLN cc_start: 0.9633 (tp40) cc_final: 0.9363 (mm-40) REVERT: C 11 MET cc_start: 0.9486 (mmp) cc_final: 0.9109 (mmp) REVERT: C 27 TYR cc_start: 0.7223 (t80) cc_final: 0.5575 (t80) REVERT: C 28 GLU cc_start: 0.9013 (pm20) cc_final: 0.8574 (pm20) REVERT: C 35 ASN cc_start: 0.9473 (m-40) cc_final: 0.9256 (t0) REVERT: C 80 LEU cc_start: 0.9737 (tp) cc_final: 0.9485 (tp) REVERT: C 82 LEU cc_start: 0.9231 (tp) cc_final: 0.9016 (tp) REVERT: C 97 ASN cc_start: 0.9422 (t0) cc_final: 0.9016 (p0) REVERT: D 87 TYR cc_start: 0.9344 (m-80) cc_final: 0.8922 (m-80) REVERT: D 97 PHE cc_start: 0.8350 (m-80) cc_final: 0.8130 (m-80) REVERT: E 9 TYR cc_start: 0.8882 (m-10) cc_final: 0.8019 (m-80) REVERT: E 15 TRP cc_start: 0.8291 (m-90) cc_final: 0.7826 (m-90) REVERT: E 65 MET cc_start: 0.9133 (ppp) cc_final: 0.8778 (ppp) REVERT: E 74 MET cc_start: 0.9582 (ppp) cc_final: 0.9333 (ppp) REVERT: E 76 GLU cc_start: 0.9648 (mm-30) cc_final: 0.9403 (mm-30) REVERT: E 118 MET cc_start: 0.8123 (mmp) cc_final: 0.7244 (tpp) REVERT: E 121 MET cc_start: 0.8887 (mmp) cc_final: 0.7915 (tpp) REVERT: E 156 ASN cc_start: 0.9171 (t0) cc_final: 0.8924 (p0) REVERT: E 395 MET cc_start: 0.9618 (ppp) cc_final: 0.9203 (ppp) REVERT: E 400 ILE cc_start: 0.9262 (mt) cc_final: 0.8988 (pt) REVERT: E 437 MET cc_start: 0.9350 (mmt) cc_final: 0.8559 (tpp) REVERT: E 441 TRP cc_start: 0.9331 (m-10) cc_final: 0.8400 (m-90) REVERT: F 566 LEU cc_start: 0.9395 (mt) cc_final: 0.9020 (tt) REVERT: F 587 TRP cc_start: 0.8879 (m100) cc_final: 0.8463 (m100) REVERT: G 27 TYR cc_start: 0.7883 (t80) cc_final: 0.7455 (t80) REVERT: G 28 GLU cc_start: 0.9680 (mp0) cc_final: 0.9431 (tp30) REVERT: G 97 ASN cc_start: 0.9383 (t0) cc_final: 0.9037 (p0) REVERT: H 87 TYR cc_start: 0.9438 (m-80) cc_final: 0.8840 (m-80) REVERT: I 65 MET cc_start: 0.9456 (ppp) cc_final: 0.9235 (ppp) REVERT: I 121 MET cc_start: 0.9523 (tpt) cc_final: 0.9323 (tpp) REVERT: I 156 ASN cc_start: 0.9197 (t0) cc_final: 0.8927 (p0) REVERT: I 239 ILE cc_start: 0.9442 (mm) cc_final: 0.9098 (mm) REVERT: I 316 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9191 (mm-30) REVERT: I 350 PHE cc_start: 0.8912 (m-80) cc_final: 0.8675 (m-80) REVERT: I 395 MET cc_start: 0.9565 (ppp) cc_final: 0.9062 (ppp) REVERT: I 400 ILE cc_start: 0.9426 (mt) cc_final: 0.9203 (pt) REVERT: I 454 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8562 (mp0) REVERT: J 544 VAL cc_start: 0.9846 (p) cc_final: 0.9507 (p) REVERT: J 548 GLU cc_start: 0.9506 (tt0) cc_final: 0.9188 (mt-10) REVERT: J 549 ARG cc_start: 0.9608 (mmt90) cc_final: 0.9130 (mmm160) REVERT: J 553 ASP cc_start: 0.9090 (m-30) cc_final: 0.8755 (m-30) REVERT: J 595 TRP cc_start: 0.9216 (t60) cc_final: 0.8569 (t60) REVERT: J 602 TYR cc_start: 0.9656 (m-10) cc_final: 0.9402 (m-80) REVERT: K 11 MET cc_start: 0.9673 (mmp) cc_final: 0.9386 (mmp) REVERT: K 27 TYR cc_start: 0.7770 (t80) cc_final: 0.7442 (t80) REVERT: K 28 GLU cc_start: 0.9768 (mp0) cc_final: 0.9557 (mp0) REVERT: K 29 PHE cc_start: 0.8863 (t80) cc_final: 0.8624 (t80) REVERT: K 51 LEU cc_start: 0.9406 (tp) cc_final: 0.9162 (tp) REVERT: K 80 LEU cc_start: 0.9688 (tp) cc_final: 0.9377 (tp) REVERT: K 82 LEU cc_start: 0.9247 (tp) cc_final: 0.9035 (tp) REVERT: K 97 ASN cc_start: 0.9423 (t0) cc_final: 0.9069 (p0) REVERT: L 87 TYR cc_start: 0.9318 (m-80) cc_final: 0.8929 (m-80) REVERT: L 89 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7766 (pm20) outliers start: 4 outliers final: 1 residues processed: 405 average time/residue: 0.1493 time to fit residues: 91.4831 Evaluate side-chains 326 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 324 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 215 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 HIS C 35 ASN D 42 GLN E 127 ASN E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN E 318 GLN E 344 ASN E 353 ASN E 440 ASN G 64 GLN H 38 GLN I 84 GLN I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 305 GLN I 440 ASN L 38 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.051347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.041676 restraints weight = 146616.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.043256 restraints weight = 92140.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.044410 restraints weight = 64863.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.045321 restraints weight = 49036.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.045999 restraints weight = 39117.507| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.6909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18879 Z= 0.220 Angle : 0.759 8.728 25646 Z= 0.411 Chirality : 0.046 0.197 2814 Planarity : 0.006 0.075 3281 Dihedral : 6.771 35.333 2530 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.27 % Favored : 91.60 % Rotamer: Outliers : 0.15 % Allowed : 3.58 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -2.02 (0.17), residues: 2297 helix: -0.79 (0.23), residues: 410 sheet: -1.15 (0.21), residues: 624 loop : -1.61 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 54 TYR 0.027 0.002 TYR G 100 PHE 0.027 0.003 PHE E 349 TRP 0.032 0.003 TRP A 388 HIS 0.005 0.001 HIS K 102 Details of bonding type rmsd covalent geometry : bond 0.00462 (18841) covalent geometry : angle 0.75441 (25570) SS BOND : bond 0.00550 ( 38) SS BOND : angle 1.70721 ( 76) hydrogen bonds : bond 0.04116 ( 597) hydrogen bonds : angle 6.14500 ( 1623) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 374 time to evaluate : 0.768 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: 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: 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: symmetry clash REVERT: A 9 TYR cc_start: 0.9132 (m-80) cc_final: 0.8361 (m-80) REVERT: A 39 TRP cc_start: 0.7885 (m-90) cc_final: 0.7380 (m-90) REVERT: A 66 TRP cc_start: 0.9444 (m100) cc_final: 0.8750 (m100) REVERT: A 74 MET cc_start: 0.9478 (tmm) cc_final: 0.9260 (tmm) REVERT: A 76 GLU cc_start: 0.9615 (mm-30) cc_final: 0.9357 (mm-30) REVERT: A 118 MET cc_start: 0.8345 (mmp) cc_final: 0.8070 (tpp) REVERT: A 121 MET cc_start: 0.9122 (mmp) cc_final: 0.8518 (tpp) REVERT: A 395 MET cc_start: 0.9592 (ppp) cc_final: 0.9246 (ppp) REVERT: A 415 LEU cc_start: 0.9599 (mt) cc_final: 0.9328 (tp) REVERT: B 548 GLU cc_start: 0.9385 (tt0) cc_final: 0.9163 (tt0) REVERT: B 553 ASP cc_start: 0.9216 (m-30) cc_final: 0.8927 (m-30) REVERT: B 554 GLN cc_start: 0.9448 (mm-40) cc_final: 0.9079 (mm110) REVERT: B 618 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8522 (tm-30) REVERT: C 11 MET cc_start: 0.9515 (mmp) cc_final: 0.9131 (mmp) REVERT: C 27 TYR cc_start: 0.7620 (t80) cc_final: 0.5885 (t80) REVERT: C 28 GLU cc_start: 0.9149 (pm20) cc_final: 0.8712 (pm20) REVERT: C 51 LEU cc_start: 0.9527 (tp) cc_final: 0.9272 (tp) REVERT: C 80 LEU cc_start: 0.9723 (tp) cc_final: 0.9503 (tp) REVERT: C 97 ASN cc_start: 0.9469 (t0) cc_final: 0.9094 (p0) REVERT: D 36 TYR cc_start: 0.8659 (m-80) cc_final: 0.7765 (m-80) REVERT: D 87 TYR cc_start: 0.9357 (m-80) cc_final: 0.8848 (m-80) REVERT: E 9 TYR cc_start: 0.9453 (m-10) cc_final: 0.8750 (m-80) REVERT: E 15 TRP cc_start: 0.8583 (m-90) cc_final: 0.7959 (m-90) REVERT: E 65 MET cc_start: 0.9238 (ppp) cc_final: 0.8883 (ppp) REVERT: E 74 MET cc_start: 0.9572 (ppp) cc_final: 0.9290 (ppp) REVERT: E 76 GLU cc_start: 0.9655 (mm-30) cc_final: 0.9381 (mm-30) REVERT: E 121 MET cc_start: 0.8927 (mmp) cc_final: 0.8165 (tpp) REVERT: E 156 ASN cc_start: 0.9249 (t0) cc_final: 0.9024 (p0) REVERT: E 395 MET cc_start: 0.9619 (ppp) cc_final: 0.9239 (ppp) REVERT: E 400 ILE cc_start: 0.9298 (mt) cc_final: 0.9073 (pt) REVERT: E 437 MET cc_start: 0.9395 (mmt) cc_final: 0.8675 (tpp) REVERT: E 441 TRP cc_start: 0.9177 (m-10) cc_final: 0.8464 (m-90) REVERT: G 18 MET cc_start: 0.9659 (tmm) cc_final: 0.9186 (tmm) REVERT: G 27 TYR cc_start: 0.7988 (t80) cc_final: 0.7674 (t80) REVERT: G 51 LEU cc_start: 0.9593 (tp) cc_final: 0.9217 (tp) REVERT: G 69 MET cc_start: 0.9202 (pmm) cc_final: 0.8846 (pmm) REVERT: G 80 LEU cc_start: 0.9728 (tt) cc_final: 0.9418 (tt) REVERT: G 82 LEU cc_start: 0.9271 (tp) cc_final: 0.8708 (tp) REVERT: G 97 ASN cc_start: 0.9400 (t0) cc_final: 0.9064 (p0) REVERT: H 36 TYR cc_start: 0.9301 (m-80) cc_final: 0.8976 (m-80) REVERT: H 38 GLN cc_start: 0.9545 (OUTLIER) cc_final: 0.9335 (pp30) REVERT: H 87 TYR cc_start: 0.9398 (m-80) cc_final: 0.8724 (m-80) REVERT: I 9 TYR cc_start: 0.9511 (m-80) cc_final: 0.9036 (m-80) REVERT: I 121 MET cc_start: 0.9544 (tpt) cc_final: 0.9197 (mmm) REVERT: I 156 ASN cc_start: 0.9237 (t0) cc_final: 0.9024 (p0) REVERT: I 251 LYS cc_start: 0.8868 (mmpt) cc_final: 0.8624 (tppt) REVERT: I 312 GLU cc_start: 0.9648 (mt-10) cc_final: 0.9376 (mm-30) REVERT: I 395 MET cc_start: 0.9604 (ppp) cc_final: 0.9050 (ppp) REVERT: I 400 ILE cc_start: 0.9401 (mt) cc_final: 0.9172 (pt) REVERT: I 414 LEU cc_start: 0.9459 (mt) cc_final: 0.9195 (mt) REVERT: I 415 LEU cc_start: 0.9601 (mt) cc_final: 0.9219 (tp) REVERT: I 454 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8421 (mp0) REVERT: J 548 GLU cc_start: 0.9457 (tt0) cc_final: 0.9055 (tm-30) REVERT: J 549 ARG cc_start: 0.9585 (mmt90) cc_final: 0.8941 (mmm160) REVERT: J 554 GLN cc_start: 0.9256 (mm-40) cc_final: 0.9027 (mm110) REVERT: J 556 LEU cc_start: 0.9670 (tp) cc_final: 0.9436 (pp) REVERT: K 11 MET cc_start: 0.9620 (mmp) cc_final: 0.9185 (mmp) REVERT: K 27 TYR cc_start: 0.7884 (t80) cc_final: 0.5792 (t80) REVERT: K 28 GLU cc_start: 0.9723 (mp0) cc_final: 0.9064 (pm20) REVERT: K 31 ASP cc_start: 0.9412 (m-30) cc_final: 0.9113 (m-30) REVERT: K 48 MET cc_start: 0.9361 (mmp) cc_final: 0.9114 (mmm) REVERT: K 51 LEU cc_start: 0.9458 (tp) cc_final: 0.9145 (tp) REVERT: K 97 ASN cc_start: 0.9304 (t0) cc_final: 0.8945 (p0) REVERT: L 87 TYR cc_start: 0.9290 (m-80) cc_final: 0.8817 (m-80) outliers start: 3 outliers final: 0 residues processed: 377 average time/residue: 0.1438 time to fit residues: 82.9566 Evaluate side-chains 293 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 141 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 chunk 121 optimal weight: 0.0370 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 201 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 ASN E 440 ASN I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 344 ASN ** I 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.054347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.043949 restraints weight = 138573.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.045652 restraints weight = 87534.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.046911 restraints weight = 61841.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.047841 restraints weight = 46744.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.048571 restraints weight = 37665.688| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.7077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18879 Z= 0.123 Angle : 0.683 7.355 25646 Z= 0.362 Chirality : 0.046 0.203 2814 Planarity : 0.005 0.082 3281 Dihedral : 6.203 36.493 2530 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.75 % Favored : 93.16 % Rotamer: Outliers : 0.10 % Allowed : 2.26 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.17), residues: 2297 helix: -0.26 (0.26), residues: 390 sheet: -0.94 (0.21), residues: 628 loop : -1.59 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 277 TYR 0.020 0.001 TYR G 100 PHE 0.033 0.002 PHE I 430 TRP 0.035 0.002 TRP B 595 HIS 0.002 0.001 HIS I 256 Details of bonding type rmsd covalent geometry : bond 0.00269 (18841) covalent geometry : angle 0.68003 (25570) SS BOND : bond 0.00370 ( 38) SS BOND : angle 1.42887 ( 76) hydrogen bonds : bond 0.03428 ( 597) hydrogen bonds : angle 5.58872 ( 1623) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 408 time to evaluate : 0.744 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: 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: 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: symmetry clash REVERT: A 9 TYR cc_start: 0.8930 (m-80) cc_final: 0.8488 (m-80) REVERT: A 10 TYR cc_start: 0.8802 (t80) cc_final: 0.7117 (p90) REVERT: A 74 MET cc_start: 0.9548 (tmm) cc_final: 0.9286 (ppp) REVERT: A 87 LYS cc_start: 0.9612 (ptpp) cc_final: 0.9379 (pttt) REVERT: A 118 MET cc_start: 0.8127 (mmp) cc_final: 0.7636 (tpp) REVERT: A 121 MET cc_start: 0.8883 (mmp) cc_final: 0.8422 (tpp) REVERT: A 239 ILE cc_start: 0.9407 (mm) cc_final: 0.8132 (mm) REVERT: A 316 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8429 (mt-10) REVERT: A 389 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8447 (pp30) REVERT: A 395 MET cc_start: 0.9535 (ppp) cc_final: 0.9245 (ppp) REVERT: A 415 LEU cc_start: 0.9551 (mt) cc_final: 0.9296 (tp) REVERT: A 440 ASN cc_start: 0.9486 (p0) cc_final: 0.9212 (p0) REVERT: B 548 GLU cc_start: 0.9385 (tt0) cc_final: 0.9099 (tt0) REVERT: B 550 TYR cc_start: 0.9512 (t80) cc_final: 0.9281 (t80) REVERT: C 11 MET cc_start: 0.9468 (mmp) cc_final: 0.9035 (mmp) REVERT: C 27 TYR cc_start: 0.7761 (t80) cc_final: 0.5552 (t80) REVERT: C 28 GLU cc_start: 0.9244 (pm20) cc_final: 0.8765 (pm20) REVERT: C 31 ASP cc_start: 0.9342 (t0) cc_final: 0.8810 (t0) REVERT: C 35 ASN cc_start: 0.9340 (m110) cc_final: 0.9109 (t0) REVERT: C 51 LEU cc_start: 0.9374 (tp) cc_final: 0.9121 (tp) REVERT: C 80 LEU cc_start: 0.9702 (tp) cc_final: 0.9459 (tp) REVERT: C 86 ASP cc_start: 0.9288 (m-30) cc_final: 0.9070 (m-30) REVERT: C 97 ASN cc_start: 0.9560 (t0) cc_final: 0.9266 (p0) REVERT: C 101 GLU cc_start: 0.9485 (tp30) cc_final: 0.9224 (tt0) REVERT: D 87 TYR cc_start: 0.9348 (m-80) cc_final: 0.8933 (m-80) REVERT: E 9 TYR cc_start: 0.9451 (m-10) cc_final: 0.8761 (m-80) REVERT: E 65 MET cc_start: 0.9197 (ppp) cc_final: 0.8859 (ppp) REVERT: E 74 MET cc_start: 0.9545 (ppp) cc_final: 0.9156 (ppp) REVERT: E 76 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9360 (mm-30) REVERT: E 121 MET cc_start: 0.8798 (mmp) cc_final: 0.8106 (tpp) REVERT: E 156 ASN cc_start: 0.9228 (t0) cc_final: 0.8952 (p0) REVERT: E 246 LEU cc_start: 0.9634 (mt) cc_final: 0.9312 (pt) REVERT: E 336 MET cc_start: 0.8486 (ppp) cc_final: 0.8235 (ppp) REVERT: E 395 MET cc_start: 0.9675 (ppp) cc_final: 0.9161 (ppp) REVERT: E 400 ILE cc_start: 0.9340 (mt) cc_final: 0.9109 (pt) REVERT: E 437 MET cc_start: 0.9474 (mmt) cc_final: 0.8735 (tpp) REVERT: E 441 TRP cc_start: 0.9183 (m-10) cc_final: 0.8218 (m-90) REVERT: F 538 LYS cc_start: 0.9702 (mmpt) cc_final: 0.9485 (mmtm) REVERT: F 565 LYS cc_start: 0.9456 (mppt) cc_final: 0.9151 (mtmm) REVERT: F 607 TYR cc_start: 0.8811 (m-80) cc_final: 0.8607 (m-80) REVERT: G 4 LEU cc_start: 0.9422 (mp) cc_final: 0.8815 (mt) REVERT: G 11 MET cc_start: 0.9564 (mmp) cc_final: 0.9349 (mmp) REVERT: G 27 TYR cc_start: 0.8493 (t80) cc_final: 0.7980 (t80) REVERT: G 69 MET cc_start: 0.9069 (pmm) cc_final: 0.8859 (pmm) REVERT: G 97 ASN cc_start: 0.9398 (t0) cc_final: 0.9032 (p0) REVERT: G 101 GLU cc_start: 0.9612 (tp30) cc_final: 0.9336 (tt0) REVERT: H 36 TYR cc_start: 0.9195 (m-80) cc_final: 0.8575 (m-80) REVERT: H 87 TYR cc_start: 0.9383 (m-80) cc_final: 0.8723 (m-80) REVERT: I 9 TYR cc_start: 0.9490 (m-80) cc_final: 0.9173 (m-10) REVERT: I 87 LYS cc_start: 0.9712 (ptpt) cc_final: 0.9494 (mtmm) REVERT: I 239 ILE cc_start: 0.9397 (mm) cc_final: 0.9078 (mm) REVERT: I 251 LYS cc_start: 0.8795 (mmpt) cc_final: 0.8581 (tppt) REVERT: I 262 GLU cc_start: 0.9589 (tt0) cc_final: 0.9363 (tp30) REVERT: I 316 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9182 (mm-30) REVERT: I 349 PHE cc_start: 0.9499 (m-10) cc_final: 0.9120 (m-10) REVERT: I 395 MET cc_start: 0.9582 (ppp) cc_final: 0.9061 (ppp) REVERT: I 400 ILE cc_start: 0.9435 (mt) cc_final: 0.9212 (pt) REVERT: I 437 MET cc_start: 0.9154 (ttt) cc_final: 0.8837 (tpp) REVERT: I 454 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8657 (mp0) REVERT: J 548 GLU cc_start: 0.9421 (tt0) cc_final: 0.9112 (mt-10) REVERT: J 556 LEU cc_start: 0.9615 (tp) cc_final: 0.9369 (pp) REVERT: K 11 MET cc_start: 0.9488 (mmp) cc_final: 0.9035 (mmp) REVERT: K 27 TYR cc_start: 0.7644 (t80) cc_final: 0.5610 (t80) REVERT: K 28 GLU cc_start: 0.9735 (mp0) cc_final: 0.9267 (pm20) REVERT: K 31 ASP cc_start: 0.9423 (m-30) cc_final: 0.9133 (t0) REVERT: K 51 LEU cc_start: 0.9400 (tp) cc_final: 0.9152 (tp) REVERT: K 52 LYS cc_start: 0.9780 (mmmm) cc_final: 0.9525 (mmtm) REVERT: K 80 LEU cc_start: 0.9691 (tp) cc_final: 0.9405 (tp) REVERT: K 97 ASN cc_start: 0.9535 (t0) cc_final: 0.9231 (p0) REVERT: L 87 TYR cc_start: 0.9292 (m-80) cc_final: 0.8814 (m-80) outliers start: 2 outliers final: 0 residues processed: 410 average time/residue: 0.1382 time to fit residues: 86.0078 Evaluate side-chains 318 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 122 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 202 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 206 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN C 102 HIS D 42 GLN E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 604 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.051753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.041912 restraints weight = 146607.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.043492 restraints weight = 92764.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.044679 restraints weight = 65765.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.045570 restraints weight = 49940.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.046263 restraints weight = 39810.982| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.7574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18879 Z= 0.182 Angle : 0.731 8.494 25646 Z= 0.389 Chirality : 0.046 0.247 2814 Planarity : 0.005 0.084 3281 Dihedral : 6.392 34.257 2530 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.84 % Favored : 92.08 % Rotamer: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.17), residues: 2297 helix: -0.52 (0.24), residues: 403 sheet: -1.14 (0.21), residues: 580 loop : -1.48 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 277 TYR 0.020 0.002 TYR G 100 PHE 0.026 0.002 PHE I 430 TRP 0.025 0.002 TRP G 100B HIS 0.005 0.001 HIS K 102 Details of bonding type rmsd covalent geometry : bond 0.00396 (18841) covalent geometry : angle 0.72591 (25570) SS BOND : bond 0.00479 ( 38) SS BOND : angle 1.75032 ( 76) hydrogen bonds : bond 0.03896 ( 597) hydrogen bonds : angle 5.95273 ( 1623) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 375 time to evaluate : 0.711 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8926 (m-80) cc_final: 0.8645 (m-80) REVERT: A 39 TRP cc_start: 0.8035 (m-90) cc_final: 0.7786 (m-90) REVERT: A 65 MET cc_start: 0.9667 (ppp) cc_final: 0.9437 (ppp) REVERT: A 78 ILE cc_start: 0.9741 (pt) cc_final: 0.9497 (pt) REVERT: A 83 ASP cc_start: 0.9670 (t70) cc_final: 0.9442 (t0) REVERT: A 87 LYS cc_start: 0.9584 (ptpp) cc_final: 0.9356 (pttt) REVERT: A 118 MET cc_start: 0.8171 (mmp) cc_final: 0.7754 (tpp) REVERT: A 121 MET cc_start: 0.8939 (mmp) cc_final: 0.8514 (tpp) REVERT: A 246 LEU cc_start: 0.9619 (mt) cc_final: 0.9296 (pt) REVERT: A 389 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8371 (pp30) REVERT: A 395 MET cc_start: 0.9559 (ppp) cc_final: 0.9234 (ppp) REVERT: A 415 LEU cc_start: 0.9592 (mt) cc_final: 0.9341 (tp) REVERT: A 440 ASN cc_start: 0.9375 (p0) cc_final: 0.9043 (p0) REVERT: B 548 GLU cc_start: 0.9365 (tt0) cc_final: 0.9036 (tt0) REVERT: B 553 ASP cc_start: 0.9207 (m-30) cc_final: 0.8981 (m-30) REVERT: C 11 MET cc_start: 0.9521 (mmp) cc_final: 0.9108 (mmp) REVERT: C 27 TYR cc_start: 0.8007 (t80) cc_final: 0.5861 (t80) REVERT: C 28 GLU cc_start: 0.9292 (pm20) cc_final: 0.8749 (pm20) REVERT: C 31 ASP cc_start: 0.9391 (t0) cc_final: 0.8864 (t0) REVERT: C 39 LEU cc_start: 0.9728 (tt) cc_final: 0.9399 (tp) REVERT: C 51 LEU cc_start: 0.9401 (tp) cc_final: 0.9188 (tp) REVERT: C 80 LEU cc_start: 0.9718 (tp) cc_final: 0.9490 (tp) REVERT: C 97 ASN cc_start: 0.9480 (t0) cc_final: 0.9216 (p0) REVERT: D 36 TYR cc_start: 0.8615 (m-80) cc_final: 0.7647 (m-80) REVERT: D 87 TYR cc_start: 0.9342 (m-80) cc_final: 0.8755 (m-80) REVERT: E 9 TYR cc_start: 0.9538 (m-10) cc_final: 0.8884 (m-80) REVERT: E 65 MET cc_start: 0.9215 (ppp) cc_final: 0.8896 (ppp) REVERT: E 74 MET cc_start: 0.9542 (ppp) cc_final: 0.9155 (ppp) REVERT: E 76 GLU cc_start: 0.9635 (mm-30) cc_final: 0.9325 (mm-30) REVERT: E 121 MET cc_start: 0.8825 (mmp) cc_final: 0.8108 (tpp) REVERT: E 156 ASN cc_start: 0.9277 (t0) cc_final: 0.9000 (p0) REVERT: E 395 MET cc_start: 0.9652 (ppp) cc_final: 0.9143 (ppp) REVERT: E 437 MET cc_start: 0.9436 (mmt) cc_final: 0.8771 (tpp) REVERT: E 441 TRP cc_start: 0.9214 (m-10) cc_final: 0.8425 (m-90) REVERT: F 538 LYS cc_start: 0.9711 (mmpt) cc_final: 0.9468 (mmtm) REVERT: F 559 ILE cc_start: 0.9486 (mt) cc_final: 0.9220 (mt) REVERT: F 565 LYS cc_start: 0.9444 (mppt) cc_final: 0.9167 (mppt) REVERT: G 27 TYR cc_start: 0.8446 (t80) cc_final: 0.8040 (t80) REVERT: G 51 LEU cc_start: 0.9527 (tp) cc_final: 0.9263 (tp) REVERT: G 69 MET cc_start: 0.9179 (pmm) cc_final: 0.8923 (pmm) REVERT: G 97 ASN cc_start: 0.9547 (t0) cc_final: 0.9251 (p0) REVERT: G 100 ASP cc_start: 0.8488 (p0) cc_final: 0.8133 (m-30) REVERT: H 86 TYR cc_start: 0.9609 (m-80) cc_final: 0.9371 (m-80) REVERT: H 87 TYR cc_start: 0.9418 (m-80) cc_final: 0.8684 (m-80) REVERT: I 9 TYR cc_start: 0.9520 (m-80) cc_final: 0.9089 (m-80) REVERT: I 91 LYS cc_start: 0.9303 (tmmt) cc_final: 0.9046 (tptp) REVERT: I 92 LEU cc_start: 0.9709 (mt) cc_final: 0.9435 (mt) REVERT: I 147 ASP cc_start: 0.8763 (m-30) cc_final: 0.8454 (m-30) REVERT: I 239 ILE cc_start: 0.9432 (mm) cc_final: 0.9146 (mm) REVERT: I 316 GLU cc_start: 0.9406 (mm-30) cc_final: 0.9144 (mm-30) REVERT: I 343 PHE cc_start: 0.8438 (p90) cc_final: 0.8035 (p90) REVERT: I 384 ILE cc_start: 0.9268 (mm) cc_final: 0.8754 (mm) REVERT: I 395 MET cc_start: 0.9590 (ppp) cc_final: 0.9048 (ppp) REVERT: I 400 ILE cc_start: 0.9374 (mt) cc_final: 0.9115 (pt) REVERT: I 454 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8404 (mp0) REVERT: J 548 GLU cc_start: 0.9455 (tt0) cc_final: 0.9113 (mt-10) REVERT: J 549 ARG cc_start: 0.9626 (mmm-85) cc_final: 0.9387 (mmm-85) REVERT: J 556 LEU cc_start: 0.9629 (tp) cc_final: 0.9384 (pp) REVERT: K 11 MET cc_start: 0.9525 (mmp) cc_final: 0.9024 (mmp) REVERT: K 27 TYR cc_start: 0.7802 (t80) cc_final: 0.5772 (t80) REVERT: K 28 GLU cc_start: 0.9713 (mp0) cc_final: 0.9106 (pm20) REVERT: K 31 ASP cc_start: 0.9431 (m-30) cc_final: 0.9174 (m-30) REVERT: K 48 MET cc_start: 0.9253 (mmp) cc_final: 0.9026 (mmm) REVERT: K 51 LEU cc_start: 0.9378 (tp) cc_final: 0.9146 (tp) REVERT: K 52 LYS cc_start: 0.9759 (mmmm) cc_final: 0.9514 (mmtm) REVERT: K 97 ASN cc_start: 0.9501 (t0) cc_final: 0.9189 (p0) REVERT: L 87 TYR cc_start: 0.9302 (m-80) cc_final: 0.8875 (m-80) REVERT: L 89 GLN cc_start: 0.7915 (pp30) cc_final: 0.7368 (pm20) REVERT: L 97 PHE cc_start: 0.8332 (m-80) cc_final: 0.8012 (m-80) outliers start: 2 outliers final: 0 residues processed: 377 average time/residue: 0.1391 time to fit residues: 80.6641 Evaluate side-chains 296 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 89 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 307 ASN J 604 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.050123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.041082 restraints weight = 151069.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.042529 restraints weight = 97515.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.043602 restraints weight = 70072.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.044412 restraints weight = 53825.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.045005 restraints weight = 43273.449| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.8084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18879 Z= 0.221 Angle : 0.785 8.917 25646 Z= 0.418 Chirality : 0.047 0.227 2814 Planarity : 0.006 0.089 3281 Dihedral : 6.780 36.947 2530 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.49 % Favored : 91.42 % Rotamer: Outliers : 0.15 % Allowed : 1.28 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -2.11 (0.17), residues: 2297 helix: -0.86 (0.23), residues: 405 sheet: -1.27 (0.20), residues: 633 loop : -1.64 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 39 TYR 0.038 0.002 TYR B 550 PHE 0.021 0.003 PHE I 430 TRP 0.023 0.002 TRP G 100B HIS 0.004 0.001 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00473 (18841) covalent geometry : angle 0.77870 (25570) SS BOND : bond 0.00928 ( 38) SS BOND : angle 1.91489 ( 76) hydrogen bonds : bond 0.04160 ( 597) hydrogen bonds : angle 6.27284 ( 1623) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 361 time to evaluate : 0.781 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: 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 9 TYR cc_start: 0.8919 (m-80) cc_final: 0.8620 (m-80) REVERT: A 16 LYS cc_start: 0.9446 (mmpt) cc_final: 0.9234 (mmmm) REVERT: A 20 THR cc_start: 0.8787 (t) cc_final: 0.8557 (m) REVERT: A 36 HIS cc_start: 0.8099 (m-70) cc_final: 0.7889 (m170) REVERT: A 39 TRP cc_start: 0.7932 (m-90) cc_final: 0.7653 (m-90) REVERT: A 65 MET cc_start: 0.9681 (ppp) cc_final: 0.9462 (ppp) REVERT: A 76 GLU cc_start: 0.9551 (mm-30) cc_final: 0.9336 (mm-30) REVERT: A 83 ASP cc_start: 0.9670 (t70) cc_final: 0.9345 (t0) REVERT: A 87 LYS cc_start: 0.9577 (ptpp) cc_final: 0.9359 (pttt) REVERT: A 118 MET cc_start: 0.7956 (mmp) cc_final: 0.7187 (tpp) REVERT: A 121 MET cc_start: 0.8906 (mmp) cc_final: 0.7896 (tpp) REVERT: A 246 LEU cc_start: 0.9564 (mt) cc_final: 0.9308 (pt) REVERT: A 395 MET cc_start: 0.9553 (ppp) cc_final: 0.9227 (ppp) REVERT: A 415 LEU cc_start: 0.9660 (mt) cc_final: 0.9418 (tp) REVERT: B 494 MET cc_start: 0.8797 (ttt) cc_final: 0.8045 (mmm) REVERT: B 549 ARG cc_start: 0.9566 (mtp180) cc_final: 0.9189 (mtp180) REVERT: C 11 MET cc_start: 0.9367 (mmp) cc_final: 0.8891 (mmp) REVERT: C 27 TYR cc_start: 0.8102 (t80) cc_final: 0.6792 (t80) REVERT: C 28 GLU cc_start: 0.9272 (pm20) cc_final: 0.8928 (pm20) REVERT: C 39 LEU cc_start: 0.9646 (tt) cc_final: 0.9276 (tp) REVERT: C 51 LEU cc_start: 0.9418 (tp) cc_final: 0.9203 (tp) REVERT: C 86 ASP cc_start: 0.9227 (m-30) cc_final: 0.9025 (m-30) REVERT: C 100 ASP cc_start: 0.9590 (p0) cc_final: 0.9375 (p0) REVERT: D 36 TYR cc_start: 0.8556 (m-80) cc_final: 0.7985 (m-80) REVERT: D 87 TYR cc_start: 0.9242 (m-80) cc_final: 0.8716 (m-80) REVERT: E 9 TYR cc_start: 0.9523 (m-10) cc_final: 0.9018 (m-80) REVERT: E 15 TRP cc_start: 0.8324 (m-90) cc_final: 0.8059 (m-90) REVERT: E 65 MET cc_start: 0.9234 (ppp) cc_final: 0.8921 (ppp) REVERT: E 74 MET cc_start: 0.9549 (ppp) cc_final: 0.9168 (ppp) REVERT: E 76 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9292 (mm-30) REVERT: E 121 MET cc_start: 0.8759 (mmp) cc_final: 0.8003 (tpp) REVERT: E 156 ASN cc_start: 0.9201 (t0) cc_final: 0.8983 (p0) REVERT: E 350 PHE cc_start: 0.9185 (m-10) cc_final: 0.8794 (m-80) REVERT: E 395 MET cc_start: 0.9621 (ppp) cc_final: 0.9129 (ppp) REVERT: E 437 MET cc_start: 0.9421 (mmt) cc_final: 0.8898 (tpt) REVERT: E 440 ASN cc_start: 0.9437 (m110) cc_final: 0.9185 (m-40) REVERT: E 441 TRP cc_start: 0.9125 (m-10) cc_final: 0.8473 (m-90) REVERT: F 553 ASP cc_start: 0.9489 (m-30) cc_final: 0.9287 (m-30) REVERT: F 554 GLN cc_start: 0.9541 (mm-40) cc_final: 0.9272 (mm110) REVERT: G 27 TYR cc_start: 0.8536 (t80) cc_final: 0.8216 (t80) REVERT: G 51 LEU cc_start: 0.9521 (tp) cc_final: 0.9257 (tp) REVERT: G 69 MET cc_start: 0.9258 (pmm) cc_final: 0.8969 (pmm) REVERT: G 97 ASN cc_start: 0.9508 (t0) cc_final: 0.9189 (p0) REVERT: G 100 ASP cc_start: 0.8296 (p0) cc_final: 0.8034 (m-30) REVERT: H 87 TYR cc_start: 0.9367 (m-80) cc_final: 0.8641 (m-80) REVERT: I 9 TYR cc_start: 0.9427 (m-80) cc_final: 0.9007 (m-80) REVERT: I 92 LEU cc_start: 0.9752 (mt) cc_final: 0.9490 (mt) REVERT: I 121 MET cc_start: 0.8877 (mmp) cc_final: 0.7946 (tpp) REVERT: I 239 ILE cc_start: 0.9292 (mm) cc_final: 0.9052 (mm) REVERT: I 316 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9179 (mm-30) REVERT: I 343 PHE cc_start: 0.8341 (p90) cc_final: 0.7999 (p90) REVERT: I 395 MET cc_start: 0.9541 (ppp) cc_final: 0.8989 (ppp) REVERT: I 400 ILE cc_start: 0.9329 (mt) cc_final: 0.9074 (pt) REVERT: I 415 LEU cc_start: 0.9650 (mt) cc_final: 0.9347 (tp) REVERT: I 437 MET cc_start: 0.9208 (ttt) cc_final: 0.8892 (tpp) REVERT: I 454 GLU cc_start: 0.9462 (mm-30) cc_final: 0.8637 (mp0) REVERT: J 548 GLU cc_start: 0.9420 (tt0) cc_final: 0.8967 (tm-30) REVERT: J 549 ARG cc_start: 0.9566 (mmm-85) cc_final: 0.8693 (mmm-85) REVERT: J 556 LEU cc_start: 0.9596 (tp) cc_final: 0.9350 (pp) REVERT: K 11 MET cc_start: 0.9468 (mmp) cc_final: 0.8867 (mmp) REVERT: K 27 TYR cc_start: 0.8089 (t80) cc_final: 0.7763 (t80) REVERT: K 51 LEU cc_start: 0.9470 (tp) cc_final: 0.9102 (tp) REVERT: K 52 LYS cc_start: 0.9779 (mmmm) cc_final: 0.9496 (mmtm) REVERT: K 69 MET cc_start: 0.9100 (pmm) cc_final: 0.8863 (pmm) REVERT: K 97 ASN cc_start: 0.9426 (t0) cc_final: 0.9140 (p0) REVERT: L 2 ILE cc_start: 0.7641 (tp) cc_final: 0.7440 (tp) REVERT: L 87 TYR cc_start: 0.9179 (m-80) cc_final: 0.8811 (m-80) REVERT: L 89 GLN cc_start: 0.7984 (pp30) cc_final: 0.7673 (pm20) outliers start: 3 outliers final: 0 residues processed: 364 average time/residue: 0.1419 time to fit residues: 79.5268 Evaluate side-chains 274 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 14 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.050240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.040893 restraints weight = 149661.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.042474 restraints weight = 94122.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.043627 restraints weight = 66050.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.044534 restraints weight = 49598.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.045140 restraints weight = 39334.453| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.8329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18879 Z= 0.180 Angle : 0.734 8.567 25646 Z= 0.393 Chirality : 0.046 0.217 2814 Planarity : 0.005 0.090 3281 Dihedral : 6.513 35.999 2530 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.45 % Favored : 91.51 % Rotamer: Outliers : 0.05 % Allowed : 1.03 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.17), residues: 2297 helix: -0.72 (0.24), residues: 395 sheet: -1.22 (0.21), residues: 625 loop : -1.55 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 277 TYR 0.021 0.002 TYR A 140 PHE 0.027 0.002 PHE E 349 TRP 0.025 0.002 TRP G 100B HIS 0.006 0.001 HIS K 102 Details of bonding type rmsd covalent geometry : bond 0.00391 (18841) covalent geometry : angle 0.72957 (25570) SS BOND : bond 0.00406 ( 38) SS BOND : angle 1.68710 ( 76) hydrogen bonds : bond 0.03984 ( 597) hydrogen bonds : angle 6.16758 ( 1623) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.717 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: 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: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8897 (m-80) cc_final: 0.8597 (m-80) REVERT: A 16 LYS cc_start: 0.9447 (mmpt) cc_final: 0.9175 (mmmm) REVERT: A 20 THR cc_start: 0.8672 (t) cc_final: 0.8455 (m) REVERT: A 39 TRP cc_start: 0.7957 (m-90) cc_final: 0.7546 (m-90) REVERT: A 49 PRO cc_start: 0.7289 (Cg_exo) cc_final: 0.7029 (Cg_endo) REVERT: A 65 MET cc_start: 0.9699 (ppp) cc_final: 0.9484 (ppp) REVERT: A 76 GLU cc_start: 0.9502 (mm-30) cc_final: 0.9302 (mm-30) REVERT: A 83 ASP cc_start: 0.9665 (t70) cc_final: 0.9411 (t0) REVERT: A 87 LYS cc_start: 0.9577 (ptpp) cc_final: 0.9344 (pttt) REVERT: A 118 MET cc_start: 0.7898 (mmp) cc_final: 0.7543 (tpp) REVERT: A 121 MET cc_start: 0.8894 (mmp) cc_final: 0.8385 (tpp) REVERT: A 239 ILE cc_start: 0.9429 (mm) cc_final: 0.9086 (mm) REVERT: A 246 LEU cc_start: 0.9583 (mt) cc_final: 0.9343 (pt) REVERT: A 395 MET cc_start: 0.9553 (ppp) cc_final: 0.9224 (ppp) REVERT: A 415 LEU cc_start: 0.9643 (mt) cc_final: 0.9408 (tp) REVERT: B 494 MET cc_start: 0.8815 (ttt) cc_final: 0.8019 (mmm) REVERT: B 548 GLU cc_start: 0.9423 (tt0) cc_final: 0.8921 (tm-30) REVERT: B 549 ARG cc_start: 0.9605 (mtp180) cc_final: 0.9109 (mtp180) REVERT: C 11 MET cc_start: 0.9432 (mmp) cc_final: 0.8997 (mmp) REVERT: C 27 TYR cc_start: 0.8112 (t80) cc_final: 0.6026 (t80) REVERT: C 28 GLU cc_start: 0.9284 (pm20) cc_final: 0.8782 (pm20) REVERT: C 31 ASP cc_start: 0.9397 (t0) cc_final: 0.8819 (t0) REVERT: C 39 LEU cc_start: 0.9706 (tt) cc_final: 0.9381 (tp) REVERT: C 80 LEU cc_start: 0.9728 (tp) cc_final: 0.9518 (tp) REVERT: C 86 ASP cc_start: 0.9134 (m-30) cc_final: 0.8892 (m-30) REVERT: C 100 ASP cc_start: 0.9581 (p0) cc_final: 0.9346 (p0) REVERT: D 36 TYR cc_start: 0.8483 (m-80) cc_final: 0.8188 (m-80) REVERT: D 87 TYR cc_start: 0.9290 (m-80) cc_final: 0.8753 (m-80) REVERT: E 9 TYR cc_start: 0.9499 (m-10) cc_final: 0.9077 (m-10) REVERT: E 15 TRP cc_start: 0.8477 (m-90) cc_final: 0.8124 (m-90) REVERT: E 16 LYS cc_start: 0.9251 (mmtm) cc_final: 0.8937 (mmtm) REVERT: E 65 MET cc_start: 0.9238 (ppp) cc_final: 0.8941 (ppp) REVERT: E 74 MET cc_start: 0.9538 (ppp) cc_final: 0.9173 (ppp) REVERT: E 76 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9274 (mm-30) REVERT: E 121 MET cc_start: 0.8827 (mmp) cc_final: 0.7997 (tpp) REVERT: E 156 ASN cc_start: 0.9208 (t0) cc_final: 0.8972 (p0) REVERT: E 164 ASN cc_start: 0.9093 (m110) cc_final: 0.8818 (p0) REVERT: E 350 PHE cc_start: 0.9262 (m-10) cc_final: 0.8875 (m-80) REVERT: E 395 MET cc_start: 0.9672 (ppp) cc_final: 0.9176 (ppp) REVERT: E 437 MET cc_start: 0.9411 (mmt) cc_final: 0.8927 (tpt) REVERT: E 440 ASN cc_start: 0.9462 (m110) cc_final: 0.9187 (m-40) REVERT: E 441 TRP cc_start: 0.9158 (m-10) cc_final: 0.8486 (m-90) REVERT: F 567 ILE cc_start: 0.9424 (mp) cc_final: 0.9106 (mm) REVERT: G 27 TYR cc_start: 0.8580 (t80) cc_final: 0.8238 (t80) REVERT: G 51 LEU cc_start: 0.9545 (tp) cc_final: 0.9317 (tp) REVERT: G 69 MET cc_start: 0.9183 (pmm) cc_final: 0.8901 (pmm) REVERT: G 100 ASP cc_start: 0.7967 (p0) cc_final: 0.7663 (m-30) REVERT: H 87 TYR cc_start: 0.9410 (m-80) cc_final: 0.8711 (m-80) REVERT: I 9 TYR cc_start: 0.9479 (m-80) cc_final: 0.9139 (m-80) REVERT: I 121 MET cc_start: 0.8823 (mmp) cc_final: 0.8073 (tpp) REVERT: I 147 ASP cc_start: 0.8885 (m-30) cc_final: 0.8650 (p0) REVERT: I 239 ILE cc_start: 0.9300 (mm) cc_final: 0.9008 (mm) REVERT: I 312 GLU cc_start: 0.9635 (mt-10) cc_final: 0.9377 (mt-10) REVERT: I 316 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9180 (mm-30) REVERT: I 343 PHE cc_start: 0.8342 (p90) cc_final: 0.8031 (p90) REVERT: I 388 TRP cc_start: 0.8431 (t-100) cc_final: 0.7592 (t-100) REVERT: I 395 MET cc_start: 0.9602 (ppp) cc_final: 0.9023 (ppp) REVERT: I 400 ILE cc_start: 0.9361 (mt) cc_final: 0.9109 (pt) REVERT: I 414 LEU cc_start: 0.9395 (mp) cc_final: 0.9188 (mp) REVERT: I 415 LEU cc_start: 0.9648 (mt) cc_final: 0.9344 (tp) REVERT: I 437 MET cc_start: 0.9202 (ttt) cc_final: 0.8743 (tpt) REVERT: I 454 GLU cc_start: 0.9409 (mm-30) cc_final: 0.8654 (mp0) REVERT: J 548 GLU cc_start: 0.9430 (tt0) cc_final: 0.8940 (tm-30) REVERT: J 549 ARG cc_start: 0.9592 (mmm-85) cc_final: 0.8697 (mmm-85) REVERT: J 556 LEU cc_start: 0.9601 (tp) cc_final: 0.9345 (pp) REVERT: J 616 GLN cc_start: 0.9613 (tm-30) cc_final: 0.9388 (tm-30) REVERT: K 11 MET cc_start: 0.9465 (mmp) cc_final: 0.8912 (mmp) REVERT: K 23 ARG cc_start: 0.9538 (ttm110) cc_final: 0.9278 (ptp90) REVERT: K 27 TYR cc_start: 0.8082 (t80) cc_final: 0.7663 (t80) REVERT: K 51 LEU cc_start: 0.9446 (tp) cc_final: 0.9044 (tp) REVERT: K 52 LYS cc_start: 0.9757 (mmmm) cc_final: 0.9474 (mmtm) REVERT: K 69 MET cc_start: 0.8995 (pmm) cc_final: 0.8794 (pmm) REVERT: K 97 ASN cc_start: 0.9481 (t0) cc_final: 0.9201 (p0) REVERT: L 87 TYR cc_start: 0.9219 (m-80) cc_final: 0.8967 (m-80) REVERT: L 89 GLN cc_start: 0.8118 (pp30) cc_final: 0.7695 (pm20) REVERT: L 97 PHE cc_start: 0.8452 (m-80) cc_final: 0.8207 (m-80) outliers start: 1 outliers final: 0 residues processed: 366 average time/residue: 0.1341 time to fit residues: 75.6899 Evaluate side-chains 290 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 91 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 298 HIS I 318 GLN ** I 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.048033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.039301 restraints weight = 159832.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.040750 restraints weight = 100594.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.041807 restraints weight = 71134.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.042622 restraints weight = 54080.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.043223 restraints weight = 43243.199| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.8860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 18879 Z= 0.281 Angle : 0.867 10.551 25646 Z= 0.466 Chirality : 0.049 0.228 2814 Planarity : 0.006 0.094 3281 Dihedral : 7.184 33.830 2530 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 27.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.49 % Favored : 89.42 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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 aren not related in a simple way. whole: -2.24 (0.17), residues: 2297 helix: -1.19 (0.24), residues: 387 sheet: -1.38 (0.21), residues: 581 loop : -1.63 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 133 TYR 0.041 0.003 TYR B 550 PHE 0.038 0.004 PHE E 349 TRP 0.029 0.003 TRP G 100B HIS 0.031 0.002 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00590 (18841) covalent geometry : angle 0.86215 (25570) SS BOND : bond 0.00429 ( 38) SS BOND : angle 1.92502 ( 76) hydrogen bonds : bond 0.04674 ( 597) hydrogen bonds : angle 6.80262 ( 1623) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4594 Ramachandran restraints generated. 2297 Oldfield, 0 Emsley, 2297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.728 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: 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: 0.9496 (mmpt) cc_final: 0.9252 (mmmt) REVERT: A 39 TRP cc_start: 0.8008 (m-90) cc_final: 0.7676 (m-90) REVERT: A 49 PRO cc_start: 0.7250 (Cg_exo) cc_final: 0.6979 (Cg_endo) REVERT: A 65 MET cc_start: 0.9704 (ppp) cc_final: 0.9485 (ppp) REVERT: A 76 GLU cc_start: 0.9540 (mm-30) cc_final: 0.9309 (mm-30) REVERT: A 83 ASP cc_start: 0.9671 (t70) cc_final: 0.9404 (t0) REVERT: A 87 LYS cc_start: 0.9605 (ptpp) cc_final: 0.9346 (pttt) REVERT: A 118 MET cc_start: 0.7645 (mmp) cc_final: 0.7176 (tpp) REVERT: A 121 MET cc_start: 0.8986 (mmp) cc_final: 0.8299 (tpp) REVERT: A 239 ILE cc_start: 0.8966 (mm) cc_final: 0.8723 (mm) REVERT: A 344 ASN cc_start: 0.9184 (t0) cc_final: 0.8969 (t0) REVERT: A 395 MET cc_start: 0.9554 (ppp) cc_final: 0.9260 (ppp) REVERT: A 415 LEU cc_start: 0.9641 (mt) cc_final: 0.9391 (tp) REVERT: A 440 ASN cc_start: 0.9595 (p0) cc_final: 0.9388 (p0) REVERT: B 548 GLU cc_start: 0.9462 (tt0) cc_final: 0.8981 (tm-30) REVERT: B 549 ARG cc_start: 0.9616 (mtp180) cc_final: 0.9320 (mtp180) REVERT: C 11 MET cc_start: 0.9443 (mmp) cc_final: 0.9011 (mmp) REVERT: C 27 TYR cc_start: 0.8058 (t80) cc_final: 0.6039 (t80) REVERT: C 28 GLU cc_start: 0.9223 (pm20) cc_final: 0.8731 (pm20) REVERT: C 31 ASP cc_start: 0.9419 (t0) cc_final: 0.8906 (t0) REVERT: C 39 LEU cc_start: 0.9702 (tt) cc_final: 0.9378 (tp) REVERT: C 51 LEU cc_start: 0.9381 (tp) cc_final: 0.9116 (tp) REVERT: C 99 ASP cc_start: 0.9136 (t70) cc_final: 0.8922 (t0) REVERT: D 87 TYR cc_start: 0.9258 (m-80) cc_final: 0.8831 (m-80) REVERT: E 9 TYR cc_start: 0.9564 (m-10) cc_final: 0.9062 (m-80) REVERT: E 15 TRP cc_start: 0.8558 (m-90) cc_final: 0.8232 (m-90) REVERT: E 16 LYS cc_start: 0.9246 (mmtm) cc_final: 0.8790 (mmtm) REVERT: E 49 PRO cc_start: 0.7720 (Cg_exo) cc_final: 0.7100 (Cg_endo) REVERT: E 65 MET cc_start: 0.9251 (ppp) cc_final: 0.8989 (ppp) REVERT: E 74 MET cc_start: 0.9562 (ppp) cc_final: 0.9219 (ppp) REVERT: E 83 ASP cc_start: 0.9666 (t70) cc_final: 0.9291 (t0) REVERT: E 87 LYS cc_start: 0.9570 (ptpt) cc_final: 0.9269 (ptpt) REVERT: E 121 MET cc_start: 0.9006 (mmp) cc_final: 0.8152 (tpp) REVERT: E 156 ASN cc_start: 0.9223 (t0) cc_final: 0.8987 (p0) REVERT: E 336 MET cc_start: 0.8845 (ppp) cc_final: 0.8571 (ppp) REVERT: E 350 PHE cc_start: 0.9185 (m-10) cc_final: 0.8822 (m-80) REVERT: E 387 MET cc_start: 0.8557 (tmm) cc_final: 0.7862 (ppp) REVERT: E 395 MET cc_start: 0.9706 (ppp) cc_final: 0.9008 (ppp) REVERT: E 437 MET cc_start: 0.9372 (mmt) cc_final: 0.9025 (tpt) REVERT: E 440 ASN cc_start: 0.9408 (m110) cc_final: 0.9186 (m-40) REVERT: E 441 TRP cc_start: 0.9145 (m-10) cc_final: 0.8504 (m-90) REVERT: F 554 GLN cc_start: 0.9482 (mm-40) cc_final: 0.9232 (mm110) REVERT: F 597 LYS cc_start: 0.9707 (mmtm) cc_final: 0.9503 (mmmt) REVERT: G 27 TYR cc_start: 0.8508 (t80) cc_final: 0.8207 (t80) REVERT: G 51 LEU cc_start: 0.9552 (tp) cc_final: 0.9335 (tp) REVERT: G 69 MET cc_start: 0.9199 (pmm) cc_final: 0.8876 (pmm) REVERT: G 86 ASP cc_start: 0.9304 (m-30) cc_final: 0.9077 (m-30) REVERT: H 87 TYR cc_start: 0.9439 (m-80) cc_final: 0.8708 (m-80) REVERT: I 9 TYR cc_start: 0.9546 (m-80) cc_final: 0.9259 (m-80) REVERT: I 343 PHE cc_start: 0.8291 (p90) cc_final: 0.8063 (p90) REVERT: I 387 MET cc_start: 0.8249 (tmm) cc_final: 0.7435 (ppp) REVERT: I 388 TRP cc_start: 0.8565 (t-100) cc_final: 0.7567 (t-100) REVERT: I 395 MET cc_start: 0.9627 (ppp) cc_final: 0.9095 (ppp) REVERT: I 400 ILE cc_start: 0.9329 (mt) cc_final: 0.9079 (pt) REVERT: I 414 LEU cc_start: 0.9389 (mp) cc_final: 0.9136 (mp) REVERT: I 415 LEU cc_start: 0.9662 (mt) cc_final: 0.9350 (tp) REVERT: I 437 MET cc_start: 0.9252 (ttt) cc_final: 0.8787 (tpt) REVERT: J 548 GLU cc_start: 0.9334 (tt0) cc_final: 0.8916 (tm-30) REVERT: J 549 ARG cc_start: 0.9613 (mmm-85) cc_final: 0.8807 (mmm-85) REVERT: K 11 MET cc_start: 0.9566 (mmp) cc_final: 0.9138 (mmp) REVERT: K 51 LEU cc_start: 0.9461 (tp) cc_final: 0.9118 (tp) REVERT: K 52 LYS cc_start: 0.9744 (mmmm) cc_final: 0.9458 (mmtm) REVERT: K 97 ASN cc_start: 0.9389 (t0) cc_final: 0.9010 (p0) REVERT: L 87 TYR cc_start: 0.9154 (m-80) cc_final: 0.8892 (m-80) REVERT: L 89 GLN cc_start: 0.8051 (pp30) cc_final: 0.7616 (pm20) REVERT: L 97 PHE cc_start: 0.8596 (m-80) cc_final: 0.8380 (m-80) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.1336 time to fit residues: 69.7978 Evaluate side-chains 255 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 140 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 298 HIS ** I 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.049897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.040612 restraints weight = 152662.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.042156 restraints weight = 96032.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.043306 restraints weight = 67410.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.044154 restraints weight = 51264.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.044833 restraints weight = 40865.923| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.8888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18879 Z= 0.165 Angle : 0.753 8.717 25646 Z= 0.402 Chirality : 0.047 0.204 2814 Planarity : 0.005 0.086 3281 Dihedral : 6.704 37.353 2530 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.23 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -2.01 (0.17), residues: 2297 helix: -0.79 (0.24), residues: 386 sheet: -1.16 (0.21), residues: 598 loop : -1.59 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 277 TYR 0.045 0.002 TYR B 550 PHE 0.030 0.002 PHE I 430 TRP 0.024 0.002 TRP B 595 HIS 0.013 0.001 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00360 (18841) covalent geometry : angle 0.74777 (25570) SS BOND : bond 0.00379 ( 38) SS BOND : angle 1.81091 ( 76) hydrogen bonds : bond 0.04012 ( 597) hydrogen bonds : angle 6.29755 ( 1623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2847.55 seconds wall clock time: 50 minutes 29.96 seconds (3029.96 seconds total)