Starting phenix.real_space_refine on Mon Jun 16 10:51:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sal_40273/06_2025/8sal_40273_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sal_40273/06_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_40273/06_2025/8sal_40273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sal_40273/06_2025/8sal_40273.map" model { file = "/net/cci-nas-00/data/ceres_data/8sal_40273/06_2025/8sal_40273_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sal_40273/06_2025/8sal_40273_neut.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.54, per 1000 atoms: 0.57 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: 4.18 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 3.10 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: 6.62 Time building geometry restraints manager: 5.03 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: 2.410 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 45.140 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.400 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.046 0.002 TRP J 560 HIS 0.010 0.001 HIS I 42 PHE 0.019 0.002 PHE K 100D TYR 0.063 0.002 TYR I 9 ARG 0.009 0.001 ARG I 442 Details of bonding type rmsd hydrogen bonds : bond 0.23008 ( 597) hydrogen bonds : angle 8.94198 ( 1623) SS BOND : bond 0.00327 ( 38) SS BOND : angle 1.61142 ( 76) covalent geometry : bond 0.00502 (18841) covalent geometry : angle 0.88946 (25570) *********************** 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 : 2.520 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: 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: 0.8821 (ppp) REVERT: A 70 MET cc_start: 0.9703 (ppp) cc_final: 0.9448 (ppp) REVERT: A 74 MET cc_start: 0.9620 (tmm) cc_final: 0.9277 (tmm) REVERT: A 83 ASP cc_start: 0.9733 (t70) cc_final: 0.9526 (t0) REVERT: A 121 MET cc_start: 0.9568 (tpp) cc_final: 0.9255 (tpp) REVERT: A 249 ASN cc_start: 0.9218 (p0) cc_final: 0.8746 (p0) REVERT: A 336 MET cc_start: 0.8655 (mtp) cc_final: 0.8429 (ptt) REVERT: A 350 PHE cc_start: 0.9240 (m-80) cc_final: 0.8474 (m-80) REVERT: A 357 LEU cc_start: 0.9647 (mt) cc_final: 0.9405 (mt) REVERT: A 358 PHE cc_start: 0.9391 (m-80) cc_final: 0.9046 (m-80) REVERT: A 377 LEU cc_start: 0.9621 (mt) cc_final: 0.9192 (mt) REVERT: A 395 MET cc_start: 0.9356 (ppp) cc_final: 0.9061 (ppp) REVERT: A 415 LEU cc_start: 0.9351 (mt) cc_final: 0.9095 (tp) REVERT: A 437 MET cc_start: 0.8984 (tpt) cc_final: 0.7891 (tpt) REVERT: A 454 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8300 (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: 0.8834 (pt) REVERT: B 607 TYR cc_start: 0.8406 (m-10) cc_final: 0.8143 (m-10) REVERT: C 4 LEU cc_start: 0.9354 (mt) cc_final: 0.8665 (mp) REVERT: C 36 TRP cc_start: 0.9280 (m100) cc_final: 0.8902 (m-10) REVERT: C 48 MET cc_start: 0.9403 (mmp) cc_final: 0.9118 (mmm) REVERT: C 73 VAL cc_start: 0.8327 (m) cc_final: 0.8054 (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: 0.8218 (p0) REVERT: D 60 ASP cc_start: 0.9513 (p0) cc_final: 0.9302 (t0) REVERT: D 87 TYR cc_start: 0.9233 (m-80) cc_final: 0.8917 (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: 0.9211 (ppp) REVERT: E 78 ILE cc_start: 0.9551 (mt) cc_final: 0.9264 (tp) REVERT: E 82 TRP cc_start: 0.9107 (t60) cc_final: 0.8867 (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: 0.8824 (p0) REVERT: E 298 HIS cc_start: 0.8823 (m-70) cc_final: 0.8328 (m-70) REVERT: E 306 TRP cc_start: 0.9714 (t-100) cc_final: 0.9498 (t-100) REVERT: E 343 PHE cc_start: 0.9129 (p90) cc_final: 0.7920 (p90) REVERT: E 350 PHE cc_start: 0.9258 (m-80) cc_final: 0.8275 (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: 0.8724 (ppp) REVERT: E 414 LEU cc_start: 0.9778 (mt) cc_final: 0.9482 (mt) REVERT: E 437 MET cc_start: 0.9227 (mmt) cc_final: 0.8373 (tpp) REVERT: E 441 TRP cc_start: 0.9352 (m-10) cc_final: 0.8731 (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: 0.9138 (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: 0.8762 (pmm) REVERT: G 82 LEU cc_start: 0.9384 (tt) cc_final: 0.9152 (tp) REVERT: G 97 ASN cc_start: 0.8802 (t0) cc_final: 0.8259 (p0) REVERT: H 87 TYR cc_start: 0.9343 (m-80) cc_final: 0.8977 (m-80) REVERT: I 65 MET cc_start: 0.9285 (ppp) cc_final: 0.8594 (ppp) REVERT: I 68 ASN cc_start: 0.9173 (t0) cc_final: 0.8742 (t0) REVERT: I 83 ASP cc_start: 0.9717 (t0) cc_final: 0.9515 (t0) REVERT: I 121 MET cc_start: 0.9671 (tpp) cc_final: 0.9291 (tpp) REVERT: I 156 ASN cc_start: 0.9149 (t0) cc_final: 0.8803 (p0) REVERT: I 249 ASN cc_start: 0.9150 (p0) cc_final: 0.8712 (p0) REVERT: I 298 HIS cc_start: 0.8913 (m-70) cc_final: 0.8397 (m-70) REVERT: I 306 TRP cc_start: 0.9787 (t-100) cc_final: 0.9544 (t-100) REVERT: I 328 TYR cc_start: 0.8870 (m-80) cc_final: 0.8596 (m-80) REVERT: I 343 PHE cc_start: 0.8935 (p90) cc_final: 0.7875 (p90) REVERT: I 350 PHE cc_start: 0.9231 (m-80) cc_final: 0.8372 (m-80) REVERT: I 385 ILE cc_start: 0.9349 (tp) cc_final: 0.8874 (pt) REVERT: I 395 MET cc_start: 0.9488 (ppp) cc_final: 0.8963 (ppp) REVERT: I 400 ILE cc_start: 0.9320 (mt) cc_final: 0.8820 (pt) REVERT: I 414 LEU cc_start: 0.9507 (mt) cc_final: 0.9049 (mt) REVERT: I 415 LEU cc_start: 0.9363 (mt) cc_final: 0.9137 (tp) REVERT: I 437 MET cc_start: 0.9191 (mmp) cc_final: 0.8166 (tpt) REVERT: J 547 VAL cc_start: 0.9659 (t) cc_final: 0.9303 (p) REVERT: J 599 ILE cc_start: 0.9559 (pt) cc_final: 0.8992 (pt) REVERT: K 4 LEU cc_start: 0.9235 (mt) cc_final: 0.8663 (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: 0.9008 (tp) REVERT: K 97 ASN cc_start: 0.8635 (t0) cc_final: 0.8304 (p0) REVERT: L 87 TYR cc_start: 0.9199 (m-80) cc_final: 0.8897 (m-80) outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.3576 time to fit residues: 348.4601 Evaluate side-chains 440 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 GLN ** 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 601 ASN C 64 GLN ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN E 3 ASN E 75 HIS E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS E 305 GLN H 38 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 298 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.056482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.045402 restraints weight = 129619.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.047124 restraints weight = 83888.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.048439 restraints weight = 60255.898| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18879 Z= 0.213 Angle : 0.774 9.099 25646 Z= 0.418 Chirality : 0.048 0.225 2814 Planarity : 0.006 0.109 3281 Dihedral : 7.041 39.463 2530 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.10 % Favored : 92.77 % Rotamer: Outliers : 0.44 % Allowed : 3.92 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.17), residues: 2297 helix: -0.61 (0.24), residues: 435 sheet: -1.44 (0.21), residues: 585 loop : -1.61 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 441 HIS 0.007 0.002 HIS I 185 PHE 0.034 0.003 PHE A 179 TYR 0.024 0.002 TYR C 100 ARG 0.007 0.001 ARG F 549 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 597) hydrogen bonds : angle 6.62953 ( 1623) SS BOND : bond 0.00315 ( 38) SS BOND : angle 1.47860 ( 76) covalent geometry : bond 0.00464 (18841) covalent geometry : angle 0.77052 (25570) *********************** 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 500 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 491 time to evaluate : 2.236 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: A 10 TYR cc_start: 0.8836 (t80) cc_final: 0.7536 (p90) REVERT: A 65 MET cc_start: 0.9583 (ppp) cc_final: 0.9107 (ppp) REVERT: A 162 LEU cc_start: 0.9584 (mt) cc_final: 0.9293 (mt) REVERT: A 246 LEU cc_start: 0.9561 (mt) cc_final: 0.9360 (pt) REVERT: A 251 LYS cc_start: 0.7999 (mmmt) cc_final: 0.7780 (mmtm) REVERT: A 377 LEU cc_start: 0.9402 (mt) cc_final: 0.9088 (tp) REVERT: A 389 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8638 (tm-30) REVERT: A 395 MET cc_start: 0.9520 (ppp) cc_final: 0.9214 (ppp) REVERT: A 400 ILE cc_start: 0.9150 (mt) cc_final: 0.8865 (pt) REVERT: A 415 LEU cc_start: 0.9498 (mt) cc_final: 0.9212 (tp) REVERT: A 454 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7899 (mp0) REVERT: B 548 GLU cc_start: 0.9608 (tt0) cc_final: 0.9400 (tt0) REVERT: B 549 ARG cc_start: 0.9708 (mtp180) cc_final: 0.9479 (mtp180) REVERT: B 560 TRP cc_start: 0.8652 (m-90) cc_final: 0.7296 (m-90) REVERT: B 587 TRP cc_start: 0.9067 (m100) cc_final: 0.8696 (m100) REVERT: C 27 TYR cc_start: 0.7305 (t80) cc_final: 0.4868 (t80) REVERT: C 28 GLU cc_start: 0.9756 (mp0) cc_final: 0.9295 (pm20) REVERT: C 37 ILE cc_start: 0.9736 (tt) cc_final: 0.9447 (mm) REVERT: C 39 LEU cc_start: 0.9756 (tt) cc_final: 0.9542 (mm) REVERT: C 48 MET cc_start: 0.9485 (mmp) cc_final: 0.9273 (mmm) REVERT: C 97 ASN cc_start: 0.9125 (t0) cc_final: 0.8734 (p0) REVERT: D 38 GLN cc_start: 0.9711 (OUTLIER) cc_final: 0.9499 (pp30) REVERT: D 87 TYR cc_start: 0.9390 (m-80) cc_final: 0.8998 (m-80) REVERT: E 65 MET cc_start: 0.9445 (ppp) cc_final: 0.9011 (ppp) REVERT: E 68 ASN cc_start: 0.9151 (t0) cc_final: 0.8708 (t0) REVERT: E 70 MET cc_start: 0.9617 (ppp) cc_final: 0.9415 (ppp) REVERT: E 74 MET cc_start: 0.9529 (ppp) cc_final: 0.9102 (ppp) REVERT: E 76 GLU cc_start: 0.9639 (mm-30) cc_final: 0.9400 (mm-30) REVERT: E 121 MET cc_start: 0.9334 (mmp) cc_final: 0.8606 (mmm) REVERT: E 156 ASN cc_start: 0.9158 (t0) cc_final: 0.8895 (p0) REVERT: E 162 LEU cc_start: 0.9446 (mt) cc_final: 0.9133 (mt) REVERT: E 164 ASN cc_start: 0.8946 (m110) cc_final: 0.8705 (m-40) REVERT: E 239 ILE cc_start: 0.9623 (mm) cc_final: 0.9347 (mm) REVERT: E 306 TRP cc_start: 0.9764 (t-100) cc_final: 0.9474 (t-100) REVERT: E 316 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8925 (mm-30) REVERT: E 350 PHE cc_start: 0.9278 (m-80) cc_final: 0.8821 (m-80) REVERT: E 395 MET cc_start: 0.9425 (ppp) cc_final: 0.9023 (ppp) REVERT: E 437 MET cc_start: 0.9343 (mmt) cc_final: 0.8498 (tpt) REVERT: E 441 TRP cc_start: 0.9474 (m-10) cc_final: 0.8859 (m-90) REVERT: E 445 LEU cc_start: 0.9569 (mm) cc_final: 0.9318 (mm) REVERT: F 553 ASP cc_start: 0.9163 (m-30) cc_final: 0.8816 (m-30) REVERT: F 554 GLN cc_start: 0.9426 (mm-40) cc_final: 0.9162 (mm110) REVERT: F 565 LYS cc_start: 0.9404 (mmtp) cc_final: 0.9154 (ptpp) REVERT: F 566 LEU cc_start: 0.8917 (mt) cc_final: 0.8563 (tt) REVERT: F 587 TRP cc_start: 0.8708 (m100) cc_final: 0.8260 (m100) REVERT: G 27 TYR cc_start: 0.7412 (t80) cc_final: 0.6237 (t80) REVERT: G 28 GLU cc_start: 0.9737 (mp0) cc_final: 0.9341 (tp30) REVERT: G 80 LEU cc_start: 0.9717 (tp) cc_final: 0.9436 (tp) REVERT: G 97 ASN cc_start: 0.9185 (t0) cc_final: 0.8611 (p0) REVERT: H 33 LEU cc_start: 0.8010 (mt) cc_final: 0.6906 (tp) REVERT: H 36 TYR cc_start: 0.9117 (m-80) cc_final: 0.8157 (m-80) REVERT: H 87 TYR cc_start: 0.9478 (m-80) cc_final: 0.8979 (m-80) REVERT: I 16 LYS cc_start: 0.9264 (tptm) cc_final: 0.9020 (mmmm) REVERT: I 39 TRP cc_start: 0.7985 (m100) cc_final: 0.7711 (m100) REVERT: I 65 MET cc_start: 0.9417 (ppp) cc_final: 0.8821 (ppp) REVERT: I 76 GLU cc_start: 0.9683 (mm-30) cc_final: 0.9464 (mm-30) REVERT: I 156 ASN cc_start: 0.9122 (t0) cc_final: 0.8834 (p0) REVERT: I 162 LEU cc_start: 0.9641 (mt) cc_final: 0.9345 (mt) REVERT: I 298 HIS cc_start: 0.8759 (m90) cc_final: 0.8341 (m90) REVERT: I 306 TRP cc_start: 0.9757 (t-100) cc_final: 0.9437 (t-100) REVERT: I 328 TYR cc_start: 0.9167 (m-80) cc_final: 0.8907 (m-10) REVERT: I 343 PHE cc_start: 0.8561 (p90) cc_final: 0.7963 (p90) REVERT: I 350 PHE cc_start: 0.9047 (m-80) cc_final: 0.8405 (m-80) REVERT: I 395 MET cc_start: 0.9337 (ppp) cc_final: 0.8959 (ppp) REVERT: I 414 LEU cc_start: 0.9510 (mt) cc_final: 0.9133 (mt) REVERT: I 415 LEU cc_start: 0.9524 (mt) cc_final: 0.9206 (tp) REVERT: I 423 ASN cc_start: 0.0769 (OUTLIER) cc_final: 0.0515 (t0) REVERT: I 437 MET cc_start: 0.8957 (mmp) cc_final: 0.8684 (tpt) REVERT: I 454 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8496 (mm-30) REVERT: J 545 LEU cc_start: 0.9770 (mm) cc_final: 0.9524 (mm) REVERT: J 548 GLU cc_start: 0.9664 (tt0) cc_final: 0.9410 (pt0) REVERT: J 599 ILE cc_start: 0.9327 (pt) cc_final: 0.8844 (pt) REVERT: J 606 ILE cc_start: 0.8164 (pt) cc_final: 0.7961 (pt) REVERT: J 616 GLN cc_start: 0.9548 (tm-30) cc_final: 0.9332 (tm-30) REVERT: K 27 TYR cc_start: 0.7322 (t80) cc_final: 0.6354 (t80) REVERT: K 28 GLU cc_start: 0.9768 (mp0) cc_final: 0.9468 (pm20) REVERT: K 39 LEU cc_start: 0.9708 (tt) cc_final: 0.9381 (mm) REVERT: K 97 ASN cc_start: 0.8989 (t0) cc_final: 0.8617 (p0) REVERT: L 87 TYR cc_start: 0.9325 (m-80) cc_final: 0.9017 (m-80) outliers start: 9 outliers final: 0 residues processed: 500 average time/residue: 0.3135 time to fit residues: 232.7433 Evaluate side-chains 358 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 356 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 178 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS E 127 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN F 571 ASN G 64 GLN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN I 75 HIS ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 271 ASN I 305 GLN I 409 ASN I 423 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.052694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.042644 restraints weight = 144566.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.044235 restraints weight = 92098.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.045426 restraints weight = 65746.654| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18879 Z= 0.239 Angle : 0.793 8.967 25646 Z= 0.428 Chirality : 0.047 0.200 2814 Planarity : 0.006 0.066 3281 Dihedral : 7.064 37.257 2530 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.75 % Favored : 92.12 % Rotamer: Outliers : 0.29 % Allowed : 4.51 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.17), residues: 2297 helix: -0.85 (0.23), residues: 426 sheet: -1.32 (0.21), residues: 606 loop : -1.74 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 560 HIS 0.005 0.001 HIS A 218 PHE 0.036 0.003 PHE I 179 TYR 0.025 0.002 TYR G 100 ARG 0.008 0.001 ARG B 552 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 597) hydrogen bonds : angle 6.39344 ( 1623) SS BOND : bond 0.00483 ( 38) SS BOND : angle 1.59738 ( 76) covalent geometry : bond 0.00502 (18841) covalent geometry : angle 0.78978 (25570) *********************** 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 421 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 415 time to evaluate : 2.375 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: A 36 HIS cc_start: 0.7552 (m170) cc_final: 0.7311 (m170) REVERT: A 65 MET cc_start: 0.9617 (ppp) cc_final: 0.9268 (ppp) REVERT: A 66 TRP cc_start: 0.9467 (m100) cc_final: 0.8777 (m100) REVERT: A 118 MET cc_start: 0.8549 (mmp) cc_final: 0.8051 (mmp) REVERT: A 377 LEU cc_start: 0.9419 (mt) cc_final: 0.9185 (tp) REVERT: A 387 MET cc_start: 0.8311 (ppp) cc_final: 0.8008 (ppp) REVERT: A 388 TRP cc_start: 0.8782 (t-100) cc_final: 0.7855 (t-100) REVERT: A 389 GLN cc_start: 0.9181 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 395 MET cc_start: 0.9576 (ppp) cc_final: 0.9313 (ppp) REVERT: A 415 LEU cc_start: 0.9609 (mt) cc_final: 0.9320 (tp) REVERT: B 554 GLN cc_start: 0.9315 (mm-40) cc_final: 0.9038 (mm110) REVERT: B 606 ILE cc_start: 0.8162 (pt) cc_final: 0.7926 (pt) REVERT: B 607 TYR cc_start: 0.8652 (m-80) cc_final: 0.8383 (m-80) REVERT: B 614 GLN cc_start: 0.9665 (tp40) cc_final: 0.9341 (mm-40) REVERT: B 618 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8526 (tm-30) REVERT: C 11 MET cc_start: 0.9514 (mmp) cc_final: 0.9033 (mmp) REVERT: C 27 TYR cc_start: 0.7573 (t80) cc_final: 0.7126 (t80) REVERT: C 28 GLU cc_start: 0.9751 (mp0) cc_final: 0.9531 (mp0) REVERT: C 37 ILE cc_start: 0.9737 (tt) cc_final: 0.9366 (mm) REVERT: C 97 ASN cc_start: 0.9436 (t0) cc_final: 0.9098 (p0) REVERT: D 87 TYR cc_start: 0.9415 (m-80) cc_final: 0.8938 (m-80) REVERT: E 9 TYR cc_start: 0.9030 (m-10) cc_final: 0.8426 (m-80) REVERT: E 15 TRP cc_start: 0.8603 (m-90) cc_final: 0.8108 (m-90) REVERT: E 39 TRP cc_start: 0.7992 (m-90) cc_final: 0.7790 (m-90) REVERT: E 65 MET cc_start: 0.9153 (ppp) cc_final: 0.8848 (ppp) REVERT: E 76 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9411 (mm-30) REVERT: E 118 MET cc_start: 0.8498 (mmp) cc_final: 0.8181 (mmp) REVERT: E 156 ASN cc_start: 0.9168 (t0) cc_final: 0.8866 (p0) REVERT: E 316 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8800 (mt-10) REVERT: E 395 MET cc_start: 0.9530 (ppp) cc_final: 0.9142 (ppp) REVERT: E 437 MET cc_start: 0.9290 (mmt) cc_final: 0.8999 (tpt) REVERT: F 549 ARG cc_start: 0.9336 (mmm160) cc_final: 0.8669 (tpm170) REVERT: F 553 ASP cc_start: 0.9107 (m-30) cc_final: 0.8123 (m-30) REVERT: F 554 GLN cc_start: 0.9302 (mm-40) cc_final: 0.8982 (mm110) REVERT: F 565 LYS cc_start: 0.9560 (mmtp) cc_final: 0.9311 (mppt) REVERT: F 566 LEU cc_start: 0.9364 (mt) cc_final: 0.8976 (tt) REVERT: F 599 ILE cc_start: 0.9493 (pt) cc_final: 0.8950 (pt) REVERT: G 27 TYR cc_start: 0.7829 (t80) cc_final: 0.7620 (t80) REVERT: G 35 ASN cc_start: 0.9312 (m-40) cc_final: 0.8767 (t0) REVERT: G 52 LYS cc_start: 0.9701 (mmmt) cc_final: 0.9452 (mmtm) REVERT: G 82 LEU cc_start: 0.9119 (tp) cc_final: 0.8888 (tp) REVERT: G 97 ASN cc_start: 0.9275 (t0) cc_final: 0.8969 (t0) REVERT: G 100 ASP cc_start: 0.8621 (p0) cc_final: 0.8417 (m-30) REVERT: H 36 TYR cc_start: 0.9341 (m-80) cc_final: 0.8966 (m-80) REVERT: H 87 TYR cc_start: 0.9423 (m-80) cc_final: 0.8737 (m-80) REVERT: I 16 LYS cc_start: 0.9144 (tptm) cc_final: 0.8895 (mmmm) REVERT: I 65 MET cc_start: 0.9470 (ppp) cc_final: 0.9214 (ppp) REVERT: I 76 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9416 (mm-30) REVERT: I 156 ASN cc_start: 0.9167 (t0) cc_final: 0.8869 (p0) REVERT: I 164 ASN cc_start: 0.9325 (m-40) cc_final: 0.8908 (m-40) REVERT: I 298 HIS cc_start: 0.8748 (m90) cc_final: 0.8411 (m90) REVERT: I 395 MET cc_start: 0.9586 (ppp) cc_final: 0.9116 (ppp) REVERT: I 400 ILE cc_start: 0.9377 (mt) cc_final: 0.9172 (pt) REVERT: I 437 MET cc_start: 0.8953 (mmp) cc_final: 0.8729 (tpt) REVERT: I 454 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8345 (mp0) REVERT: J 548 GLU cc_start: 0.9509 (tt0) cc_final: 0.9241 (mt-10) REVERT: J 549 ARG cc_start: 0.9655 (mtp180) cc_final: 0.9356 (mmm-85) REVERT: J 553 ASP cc_start: 0.9021 (m-30) cc_final: 0.8800 (m-30) REVERT: J 554 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8936 (mm110) REVERT: J 606 ILE cc_start: 0.8162 (pt) cc_final: 0.7960 (pt) REVERT: J 607 TYR cc_start: 0.8347 (m-80) cc_final: 0.8131 (m-80) REVERT: J 616 GLN cc_start: 0.9582 (tm-30) cc_final: 0.9369 (tm-30) REVERT: K 11 MET cc_start: 0.9661 (mmp) cc_final: 0.9227 (mmp) REVERT: K 27 TYR cc_start: 0.7276 (t80) cc_final: 0.6375 (t80) REVERT: K 28 GLU cc_start: 0.9731 (mp0) cc_final: 0.9328 (pm20) REVERT: K 48 MET cc_start: 0.9361 (mmt) cc_final: 0.9119 (mmm) REVERT: K 69 MET cc_start: 0.8789 (pmm) cc_final: 0.8498 (pmm) REVERT: K 97 ASN cc_start: 0.9292 (t0) cc_final: 0.9090 (p0) REVERT: L 87 TYR cc_start: 0.9269 (m-80) cc_final: 0.8911 (m-80) outliers start: 6 outliers final: 2 residues processed: 420 average time/residue: 0.3112 time to fit residues: 194.2331 Evaluate side-chains 314 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 312 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 157 optimal weight: 20.0000 chunk 213 optimal weight: 5.9990 chunk 206 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 215 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 409 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** F 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 ASN I 440 ASN L 38 GLN L 89 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.043685 restraints weight = 140483.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.045360 restraints weight = 88695.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.046609 restraints weight = 62903.485| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18879 Z= 0.147 Angle : 0.701 8.248 25646 Z= 0.376 Chirality : 0.047 0.223 2814 Planarity : 0.005 0.073 3281 Dihedral : 6.561 35.827 2530 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.75 % Favored : 93.12 % Rotamer: Outliers : 0.15 % Allowed : 3.87 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.17), residues: 2297 helix: -0.30 (0.25), residues: 400 sheet: -1.08 (0.21), residues: 614 loop : -1.53 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 441 HIS 0.015 0.001 HIS K 102 PHE 0.022 0.002 PHE A 179 TYR 0.022 0.002 TYR E 140 ARG 0.014 0.001 ARG I 277 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 597) hydrogen bonds : angle 5.88897 ( 1623) SS BOND : bond 0.00565 ( 38) SS BOND : angle 1.59171 ( 76) covalent geometry : bond 0.00320 (18841) covalent geometry : angle 0.69664 (25570) *********************** 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 424 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 421 time to evaluate : 3.052 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: A 9 TYR cc_start: 0.9198 (m-80) cc_final: 0.8731 (m-80) REVERT: A 36 HIS cc_start: 0.7502 (m170) cc_final: 0.7253 (m170) REVERT: A 65 MET cc_start: 0.9695 (ppp) cc_final: 0.9292 (ppp) REVERT: A 66 TRP cc_start: 0.9492 (m100) cc_final: 0.8800 (m100) REVERT: A 118 MET cc_start: 0.8491 (mmp) cc_final: 0.7783 (mmp) REVERT: A 121 MET cc_start: 0.9098 (mmp) cc_final: 0.8431 (tpp) REVERT: A 195 LEU cc_start: 0.9526 (mp) cc_final: 0.9258 (mp) REVERT: A 344 ASN cc_start: 0.8997 (t0) cc_final: 0.8784 (t0) REVERT: A 377 LEU cc_start: 0.9519 (mt) cc_final: 0.9220 (tp) REVERT: A 388 TRP cc_start: 0.8838 (t-100) cc_final: 0.8056 (t-100) REVERT: A 389 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 395 MET cc_start: 0.9589 (ppp) cc_final: 0.9324 (ppp) REVERT: A 415 LEU cc_start: 0.9683 (mt) cc_final: 0.9413 (tp) REVERT: A 441 TRP cc_start: 0.9094 (m-90) cc_final: 0.8452 (m-90) REVERT: A 454 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8313 (mp0) REVERT: B 549 ARG cc_start: 0.9611 (mtt-85) cc_final: 0.9373 (mmm-85) REVERT: B 554 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9217 (mm110) REVERT: C 11 MET cc_start: 0.9585 (mmp) cc_final: 0.9098 (mmp) REVERT: C 27 TYR cc_start: 0.7765 (t80) cc_final: 0.6883 (t80) REVERT: C 28 GLU cc_start: 0.9742 (mp0) cc_final: 0.9231 (tp30) REVERT: C 37 ILE cc_start: 0.9726 (tt) cc_final: 0.9453 (mm) REVERT: C 97 ASN cc_start: 0.9377 (t0) cc_final: 0.9039 (p0) REVERT: C 100 ASP cc_start: 0.9674 (p0) cc_final: 0.9416 (p0) REVERT: D 87 TYR cc_start: 0.9395 (m-80) cc_final: 0.9158 (m-80) REVERT: D 97 PHE cc_start: 0.8464 (m-80) cc_final: 0.8244 (m-80) REVERT: E 9 TYR cc_start: 0.9280 (m-10) cc_final: 0.8615 (m-80) REVERT: E 65 MET cc_start: 0.9167 (ppp) cc_final: 0.8833 (ppp) REVERT: E 74 MET cc_start: 0.9627 (ppp) cc_final: 0.9219 (ppp) REVERT: E 76 GLU cc_start: 0.9664 (mm-30) cc_final: 0.9398 (mm-30) REVERT: E 118 MET cc_start: 0.8400 (mmp) cc_final: 0.8130 (mmp) REVERT: E 121 MET cc_start: 0.9366 (mmp) cc_final: 0.8972 (mmm) REVERT: E 147 ASP cc_start: 0.9161 (m-30) cc_final: 0.8930 (m-30) REVERT: E 156 ASN cc_start: 0.9216 (t0) cc_final: 0.8958 (p0) REVERT: E 162 LEU cc_start: 0.9253 (tp) cc_final: 0.8893 (tp) REVERT: E 316 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8718 (mt-10) REVERT: E 395 MET cc_start: 0.9597 (ppp) cc_final: 0.9184 (ppp) REVERT: E 437 MET cc_start: 0.9221 (mmt) cc_final: 0.8611 (tpt) REVERT: E 441 TRP cc_start: 0.9340 (m-10) cc_final: 0.8613 (m-90) REVERT: F 587 TRP cc_start: 0.8843 (m100) cc_final: 0.8401 (m100) REVERT: F 612 GLU cc_start: 0.9734 (pp20) cc_final: 0.9446 (mp0) REVERT: G 11 MET cc_start: 0.9504 (mmp) cc_final: 0.9290 (mmp) REVERT: G 27 TYR cc_start: 0.7996 (t80) cc_final: 0.7785 (t80) REVERT: G 35 ASN cc_start: 0.9292 (m-40) cc_final: 0.8871 (t0) REVERT: G 51 LEU cc_start: 0.9579 (tp) cc_final: 0.9245 (tp) REVERT: G 100 ASP cc_start: 0.8501 (p0) cc_final: 0.8262 (m-30) REVERT: G 101 GLU cc_start: 0.9642 (tp30) cc_final: 0.9393 (tt0) REVERT: H 36 TYR cc_start: 0.9293 (m-80) cc_final: 0.8933 (m-80) REVERT: H 87 TYR cc_start: 0.9454 (m-80) cc_final: 0.8852 (m-80) REVERT: I 16 LYS cc_start: 0.9169 (tptm) cc_final: 0.8893 (mmmm) REVERT: I 65 MET cc_start: 0.9455 (ppp) cc_final: 0.9227 (ppp) REVERT: I 76 GLU cc_start: 0.9623 (mm-30) cc_final: 0.9399 (mm-30) REVERT: I 121 MET cc_start: 0.8932 (mmp) cc_final: 0.7476 (tpp) REVERT: I 156 ASN cc_start: 0.9223 (t0) cc_final: 0.8943 (p0) REVERT: I 162 LEU cc_start: 0.8901 (tp) cc_final: 0.8525 (tp) REVERT: I 164 ASN cc_start: 0.9052 (m-40) cc_final: 0.8844 (m-40) REVERT: I 239 ILE cc_start: 0.9405 (mm) cc_final: 0.9072 (mm) REVERT: I 262 GLU cc_start: 0.9513 (tt0) cc_final: 0.9236 (tm-30) REVERT: I 316 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9171 (mm-30) REVERT: I 395 MET cc_start: 0.9637 (ppp) cc_final: 0.9129 (ppp) REVERT: I 400 ILE cc_start: 0.9379 (mt) cc_final: 0.9131 (pt) REVERT: I 413 LEU cc_start: 0.9774 (mt) cc_final: 0.9559 (mt) REVERT: I 415 LEU cc_start: 0.9596 (mp) cc_final: 0.9011 (tp) REVERT: I 454 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8623 (mm-30) REVERT: J 548 GLU cc_start: 0.9502 (tt0) cc_final: 0.9174 (mt-10) REVERT: J 553 ASP cc_start: 0.9069 (m-30) cc_final: 0.8866 (m-30) REVERT: J 606 ILE cc_start: 0.8110 (pt) cc_final: 0.7836 (pt) REVERT: J 607 TYR cc_start: 0.8510 (m-80) cc_final: 0.8138 (m-80) REVERT: K 11 MET cc_start: 0.9593 (mmp) cc_final: 0.9062 (mmp) REVERT: K 27 TYR cc_start: 0.7848 (t80) cc_final: 0.7563 (t80) REVERT: K 28 GLU cc_start: 0.9754 (mp0) cc_final: 0.9516 (mp0) REVERT: K 48 MET cc_start: 0.9365 (mmt) cc_final: 0.9128 (mmm) REVERT: K 80 LEU cc_start: 0.9707 (tt) cc_final: 0.9498 (tt) REVERT: K 97 ASN cc_start: 0.9364 (t0) cc_final: 0.9112 (p0) REVERT: L 87 TYR cc_start: 0.9265 (m-80) cc_final: 0.8881 (m-80) outliers start: 3 outliers final: 0 residues processed: 423 average time/residue: 0.3270 time to fit residues: 205.2894 Evaluate side-chains 317 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** C 102 HIS ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN F 614 GLN G 64 GLN H 38 GLN ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 344 ASN ** I 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.051748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.041958 restraints weight = 148222.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.043551 restraints weight = 93284.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.044742 restraints weight = 66032.696| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.6872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18879 Z= 0.209 Angle : 0.751 9.000 25646 Z= 0.404 Chirality : 0.046 0.193 2814 Planarity : 0.006 0.140 3281 Dihedral : 6.785 34.854 2530 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.92 % Favored : 91.95 % Rotamer: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.17), residues: 2297 helix: -0.67 (0.24), residues: 406 sheet: -1.16 (0.21), residues: 608 loop : -1.63 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 441 HIS 0.021 0.002 HIS K 102 PHE 0.029 0.003 PHE D 62 TYR 0.022 0.002 TYR E 140 ARG 0.008 0.001 ARG I 277 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 597) hydrogen bonds : angle 6.21117 ( 1623) SS BOND : bond 0.00399 ( 38) SS BOND : angle 1.71291 ( 76) covalent geometry : bond 0.00449 (18841) covalent geometry : angle 0.74663 (25570) *********************** 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 388 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 386 time to evaluate : 2.057 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: A 9 TYR cc_start: 0.9100 (m-80) cc_final: 0.8512 (m-80) REVERT: A 10 TYR cc_start: 0.9056 (t80) cc_final: 0.7369 (p90) REVERT: A 36 HIS cc_start: 0.7917 (m-70) cc_final: 0.7603 (m170) REVERT: A 39 TRP cc_start: 0.7940 (m-90) cc_final: 0.7617 (m-90) REVERT: A 83 ASP cc_start: 0.9733 (t70) cc_final: 0.9518 (t0) REVERT: A 118 MET cc_start: 0.8458 (mmp) cc_final: 0.7792 (mmp) REVERT: A 246 LEU cc_start: 0.9559 (mt) cc_final: 0.9263 (pt) REVERT: A 338 ILE cc_start: 0.9489 (mm) cc_final: 0.9274 (pt) REVERT: A 344 ASN cc_start: 0.9034 (t0) cc_final: 0.8823 (t0) REVERT: A 388 TRP cc_start: 0.8894 (t-100) cc_final: 0.8196 (t-100) REVERT: A 395 MET cc_start: 0.9628 (ppp) cc_final: 0.9312 (ppp) REVERT: A 415 LEU cc_start: 0.9695 (mt) cc_final: 0.9408 (tp) REVERT: A 454 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8348 (mp0) REVERT: B 549 ARG cc_start: 0.9508 (mtt-85) cc_final: 0.9306 (mmm160) REVERT: C 11 MET cc_start: 0.9644 (mmp) cc_final: 0.9150 (mmp) REVERT: C 27 TYR cc_start: 0.7695 (t80) cc_final: 0.5702 (t80) REVERT: C 28 GLU cc_start: 0.9644 (mp0) cc_final: 0.9111 (pm20) REVERT: C 37 ILE cc_start: 0.9727 (tt) cc_final: 0.9444 (mm) REVERT: C 97 ASN cc_start: 0.9449 (t0) cc_final: 0.9087 (p0) REVERT: D 87 TYR cc_start: 0.9361 (m-80) cc_final: 0.8776 (m-80) REVERT: E 9 TYR cc_start: 0.9530 (m-10) cc_final: 0.8837 (m-80) REVERT: E 15 TRP cc_start: 0.8437 (m-90) cc_final: 0.7988 (m-90) REVERT: E 65 MET cc_start: 0.9207 (ppp) cc_final: 0.8887 (ppp) REVERT: E 74 MET cc_start: 0.9602 (ppp) cc_final: 0.9080 (ppp) REVERT: E 76 GLU cc_start: 0.9615 (mm-30) cc_final: 0.9311 (mm-30) REVERT: E 87 LYS cc_start: 0.9659 (ptpt) cc_final: 0.9413 (ptpt) REVERT: E 147 ASP cc_start: 0.9155 (m-30) cc_final: 0.8917 (m-30) REVERT: E 156 ASN cc_start: 0.9243 (t0) cc_final: 0.8990 (p0) REVERT: E 162 LEU cc_start: 0.9216 (tp) cc_final: 0.8832 (tp) REVERT: E 388 TRP cc_start: 0.8544 (t-100) cc_final: 0.8003 (t-100) REVERT: E 395 MET cc_start: 0.9644 (ppp) cc_final: 0.9159 (ppp) REVERT: E 437 MET cc_start: 0.9313 (mmt) cc_final: 0.8572 (tpp) REVERT: E 441 TRP cc_start: 0.9292 (m-10) cc_final: 0.8432 (m-90) REVERT: F 549 ARG cc_start: 0.9214 (mmm160) cc_final: 0.8767 (tpm170) REVERT: F 553 ASP cc_start: 0.9264 (m-30) cc_final: 0.8576 (m-30) REVERT: F 565 LYS cc_start: 0.9466 (mppt) cc_final: 0.9211 (mppt) REVERT: G 11 MET cc_start: 0.9542 (mmp) cc_final: 0.9298 (mmp) REVERT: G 27 TYR cc_start: 0.7984 (t80) cc_final: 0.7661 (t80) REVERT: G 29 PHE cc_start: 0.8515 (t80) cc_final: 0.8300 (t80) REVERT: G 69 MET cc_start: 0.9144 (pmm) cc_final: 0.8787 (pmm) REVERT: G 80 LEU cc_start: 0.9738 (tt) cc_final: 0.9533 (tt) REVERT: G 82 LEU cc_start: 0.9259 (tp) cc_final: 0.9058 (tp) REVERT: G 97 ASN cc_start: 0.9256 (t0) cc_final: 0.9037 (t0) REVERT: G 100 ASP cc_start: 0.8236 (p0) cc_final: 0.7946 (m-30) REVERT: H 38 GLN cc_start: 0.9604 (OUTLIER) cc_final: 0.9339 (pp30) REVERT: H 87 TYR cc_start: 0.9401 (m-80) cc_final: 0.8678 (m-80) REVERT: I 9 TYR cc_start: 0.9574 (m-80) cc_final: 0.9268 (m-80) REVERT: I 15 TRP cc_start: 0.8368 (m-10) cc_final: 0.8142 (m-10) REVERT: I 76 GLU cc_start: 0.9647 (mm-30) cc_final: 0.9383 (mm-30) REVERT: I 121 MET cc_start: 0.8951 (mmp) cc_final: 0.7669 (tpp) REVERT: I 156 ASN cc_start: 0.9257 (t0) cc_final: 0.9007 (p0) REVERT: I 162 LEU cc_start: 0.8712 (tp) cc_final: 0.8426 (tp) REVERT: I 239 ILE cc_start: 0.9384 (mm) cc_final: 0.9066 (mm) REVERT: I 312 GLU cc_start: 0.9649 (mt-10) cc_final: 0.9296 (mm-30) REVERT: I 316 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9207 (mm-30) REVERT: I 395 MET cc_start: 0.9653 (ppp) cc_final: 0.9098 (ppp) REVERT: I 400 ILE cc_start: 0.9361 (mt) cc_final: 0.9114 (pt) REVERT: I 413 LEU cc_start: 0.9726 (mt) cc_final: 0.9509 (mt) REVERT: I 414 LEU cc_start: 0.9475 (mt) cc_final: 0.9186 (mt) REVERT: I 415 LEU cc_start: 0.9654 (mp) cc_final: 0.9027 (tp) REVERT: I 454 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8279 (mp0) REVERT: J 539 GLN cc_start: 0.9205 (mp10) cc_final: 0.8978 (mp10) REVERT: J 548 GLU cc_start: 0.9479 (tt0) cc_final: 0.9112 (tm-30) REVERT: J 556 LEU cc_start: 0.9657 (tp) cc_final: 0.9424 (pp) REVERT: J 606 ILE cc_start: 0.8251 (pt) cc_final: 0.8011 (pt) REVERT: J 607 TYR cc_start: 0.8487 (m-80) cc_final: 0.8145 (m-80) REVERT: K 11 MET cc_start: 0.9617 (mmp) cc_final: 0.9063 (mmp) REVERT: K 27 TYR cc_start: 0.7930 (t80) cc_final: 0.5753 (t80) REVERT: K 28 GLU cc_start: 0.9724 (mp0) cc_final: 0.9082 (pm20) REVERT: K 31 ASP cc_start: 0.9450 (m-30) cc_final: 0.9178 (m-30) REVERT: K 48 MET cc_start: 0.9396 (mmt) cc_final: 0.8868 (mtm) REVERT: K 69 MET cc_start: 0.8922 (pmm) cc_final: 0.8704 (pmm) REVERT: K 80 LEU cc_start: 0.9633 (tt) cc_final: 0.9422 (tt) REVERT: K 97 ASN cc_start: 0.9403 (t0) cc_final: 0.9123 (p0) REVERT: L 87 TYR cc_start: 0.9284 (m-80) cc_final: 0.8951 (m-80) REVERT: L 89 GLN cc_start: 0.8146 (pp30) cc_final: 0.7908 (pm20) REVERT: L 97 PHE cc_start: 0.8668 (m-80) cc_final: 0.8395 (m-80) outliers start: 2 outliers final: 0 residues processed: 388 average time/residue: 0.3103 time to fit residues: 182.3897 Evaluate side-chains 301 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 66 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN E 440 ASN I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.052787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.042862 restraints weight = 144281.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.044509 restraints weight = 90054.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.045710 restraints weight = 63334.558| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18879 Z= 0.149 Angle : 0.710 9.824 25646 Z= 0.378 Chirality : 0.046 0.210 2814 Planarity : 0.005 0.081 3281 Dihedral : 6.429 35.545 2530 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.88 % Favored : 92.99 % Rotamer: Outliers : 0.05 % Allowed : 2.26 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.17), residues: 2297 helix: -0.59 (0.25), residues: 396 sheet: -1.20 (0.21), residues: 624 loop : -1.61 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 306 HIS 0.018 0.001 HIS K 102 PHE 0.036 0.002 PHE A 430 TYR 0.021 0.002 TYR E 140 ARG 0.011 0.001 ARG E 277 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 597) hydrogen bonds : angle 6.00032 ( 1623) SS BOND : bond 0.00327 ( 38) SS BOND : angle 1.54457 ( 76) covalent geometry : bond 0.00325 (18841) covalent geometry : angle 0.70560 (25570) *********************** 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 393 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 2.072 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: A 9 TYR cc_start: 0.9083 (m-80) cc_final: 0.8435 (m-80) REVERT: A 10 TYR cc_start: 0.9208 (t80) cc_final: 0.7538 (p90) REVERT: A 16 LYS cc_start: 0.9619 (mmpt) cc_final: 0.9151 (mmmm) REVERT: A 39 TRP cc_start: 0.8021 (m-90) cc_final: 0.7591 (m-90) REVERT: A 118 MET cc_start: 0.8476 (mmp) cc_final: 0.7713 (mmp) REVERT: A 121 MET cc_start: 0.9061 (mmp) cc_final: 0.8464 (tpp) REVERT: A 246 LEU cc_start: 0.9573 (mt) cc_final: 0.9288 (pt) REVERT: A 338 ILE cc_start: 0.9420 (mm) cc_final: 0.9171 (pt) REVERT: A 344 ASN cc_start: 0.9080 (t0) cc_final: 0.8853 (t0) REVERT: A 388 TRP cc_start: 0.9060 (t-100) cc_final: 0.8176 (t-100) REVERT: A 395 MET cc_start: 0.9626 (ppp) cc_final: 0.9334 (ppp) REVERT: A 415 LEU cc_start: 0.9674 (mt) cc_final: 0.9395 (tp) REVERT: B 549 ARG cc_start: 0.9493 (mtt-85) cc_final: 0.9269 (mmm160) REVERT: B 602 TYR cc_start: 0.9579 (m-80) cc_final: 0.9348 (m-80) REVERT: B 609 LEU cc_start: 0.9372 (pt) cc_final: 0.9112 (pp) REVERT: C 11 MET cc_start: 0.9604 (mmp) cc_final: 0.9081 (mmp) REVERT: C 18 MET cc_start: 0.9324 (tmm) cc_final: 0.9122 (tmm) REVERT: C 27 TYR cc_start: 0.7996 (t80) cc_final: 0.7690 (t80) REVERT: C 97 ASN cc_start: 0.9579 (t0) cc_final: 0.9238 (p0) REVERT: D 87 TYR cc_start: 0.9378 (m-80) cc_final: 0.8698 (m-80) REVERT: E 9 TYR cc_start: 0.9533 (m-10) cc_final: 0.8937 (m-80) REVERT: E 15 TRP cc_start: 0.8370 (m-90) cc_final: 0.7976 (m-90) REVERT: E 65 MET cc_start: 0.9226 (ppp) cc_final: 0.8912 (ppp) REVERT: E 74 MET cc_start: 0.9527 (ppp) cc_final: 0.9070 (ppp) REVERT: E 76 GLU cc_start: 0.9593 (mm-30) cc_final: 0.9290 (mm-30) REVERT: E 87 LYS cc_start: 0.9618 (ptpt) cc_final: 0.9408 (ptpt) REVERT: E 92 LEU cc_start: 0.9736 (mt) cc_final: 0.9509 (mt) REVERT: E 121 MET cc_start: 0.9212 (mmm) cc_final: 0.8429 (mmm) REVERT: E 147 ASP cc_start: 0.9101 (m-30) cc_final: 0.8900 (m-30) REVERT: E 156 ASN cc_start: 0.9264 (t0) cc_final: 0.8974 (p0) REVERT: E 162 LEU cc_start: 0.9259 (tp) cc_final: 0.8879 (tp) REVERT: E 388 TRP cc_start: 0.8590 (t-100) cc_final: 0.7926 (t-100) REVERT: E 395 MET cc_start: 0.9656 (ppp) cc_final: 0.9192 (ppp) REVERT: E 437 MET cc_start: 0.9309 (mmt) cc_final: 0.8622 (tpp) REVERT: E 441 TRP cc_start: 0.9236 (m-10) cc_final: 0.8309 (m-90) REVERT: F 549 ARG cc_start: 0.9222 (mmm160) cc_final: 0.8803 (tpp-160) REVERT: F 552 ARG cc_start: 0.9174 (mtt-85) cc_final: 0.8793 (mtt-85) REVERT: F 565 LYS cc_start: 0.9451 (mppt) cc_final: 0.9203 (mppt) REVERT: G 4 LEU cc_start: 0.9423 (mt) cc_final: 0.9023 (mt) REVERT: G 11 MET cc_start: 0.9547 (mmp) cc_final: 0.9338 (mmp) REVERT: G 18 MET cc_start: 0.9630 (tmm) cc_final: 0.9378 (tmm) REVERT: G 48 MET cc_start: 0.9122 (mmp) cc_final: 0.8423 (mmm) REVERT: G 51 LEU cc_start: 0.9572 (tp) cc_final: 0.9306 (tp) REVERT: G 69 MET cc_start: 0.9044 (pmm) cc_final: 0.8699 (pmm) REVERT: G 80 LEU cc_start: 0.9702 (tt) cc_final: 0.9313 (tt) REVERT: G 82 LEU cc_start: 0.9340 (tp) cc_final: 0.8977 (tp) REVERT: G 86 ASP cc_start: 0.9289 (m-30) cc_final: 0.9085 (m-30) REVERT: G 97 ASN cc_start: 0.9165 (t0) cc_final: 0.8934 (t0) REVERT: G 100 ASP cc_start: 0.8386 (p0) cc_final: 0.7910 (m-30) REVERT: H 36 TYR cc_start: 0.9257 (m-80) cc_final: 0.8845 (m-80) REVERT: H 87 TYR cc_start: 0.9430 (m-80) cc_final: 0.8830 (m-80) REVERT: I 9 TYR cc_start: 0.9576 (m-80) cc_final: 0.9313 (m-80) REVERT: I 74 MET cc_start: 0.9778 (ppp) cc_final: 0.9422 (ppp) REVERT: I 76 GLU cc_start: 0.9623 (mm-30) cc_final: 0.9329 (mm-30) REVERT: I 121 MET cc_start: 0.9104 (mmp) cc_final: 0.8445 (tpp) REVERT: I 156 ASN cc_start: 0.9300 (t0) cc_final: 0.9081 (p0) REVERT: I 164 ASN cc_start: 0.9000 (m110) cc_final: 0.8741 (m-40) REVERT: I 239 ILE cc_start: 0.9407 (mm) cc_final: 0.7708 (mm) REVERT: I 316 GLU cc_start: 0.9381 (mm-30) cc_final: 0.8990 (mt-10) REVERT: I 395 MET cc_start: 0.9652 (ppp) cc_final: 0.9079 (ppp) REVERT: I 400 ILE cc_start: 0.9365 (mt) cc_final: 0.9117 (pt) REVERT: I 414 LEU cc_start: 0.9423 (mt) cc_final: 0.9162 (mt) REVERT: I 415 LEU cc_start: 0.9636 (mp) cc_final: 0.9061 (tp) REVERT: I 441 TRP cc_start: 0.8968 (m-10) cc_final: 0.7799 (m100) REVERT: I 454 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8784 (mm-30) REVERT: J 548 GLU cc_start: 0.9465 (tt0) cc_final: 0.8944 (tm-30) REVERT: J 551 LEU cc_start: 0.9860 (mt) cc_final: 0.9598 (pp) REVERT: J 556 LEU cc_start: 0.9620 (tp) cc_final: 0.9297 (pp) REVERT: J 607 TYR cc_start: 0.8652 (m-80) cc_final: 0.8251 (m-80) REVERT: K 11 MET cc_start: 0.9613 (mmp) cc_final: 0.9075 (mmp) REVERT: K 27 TYR cc_start: 0.7947 (t80) cc_final: 0.5753 (t80) REVERT: K 28 GLU cc_start: 0.9731 (mp0) cc_final: 0.9204 (pm20) REVERT: K 31 ASP cc_start: 0.9498 (m-30) cc_final: 0.9097 (t0) REVERT: K 69 MET cc_start: 0.8895 (pmm) cc_final: 0.8633 (pmm) REVERT: K 80 LEU cc_start: 0.9536 (tt) cc_final: 0.9102 (tt) REVERT: K 97 ASN cc_start: 0.9510 (t0) cc_final: 0.9244 (p0) REVERT: L 87 TYR cc_start: 0.9313 (m-80) cc_final: 0.9034 (m-80) REVERT: L 89 GLN cc_start: 0.8085 (pp30) cc_final: 0.7535 (pm20) REVERT: L 97 PHE cc_start: 0.8547 (m-80) cc_final: 0.8060 (m-80) outliers start: 1 outliers final: 0 residues processed: 393 average time/residue: 0.2990 time to fit residues: 177.6207 Evaluate side-chains 309 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 175 optimal weight: 20.0000 chunk 204 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 221 optimal weight: 0.0980 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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 298 HIS A 307 ASN A 356 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN E 318 GLN ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN I 52 GLN I 423 ASN I 440 ASN K 35 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.050463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.041083 restraints weight = 148781.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.042590 restraints weight = 94194.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.043679 restraints weight = 66960.322| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.7767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18879 Z= 0.212 Angle : 0.765 10.878 25646 Z= 0.410 Chirality : 0.047 0.248 2814 Planarity : 0.006 0.084 3281 Dihedral : 6.682 34.513 2530 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.34 % Rotamer: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.17), residues: 2297 helix: -0.78 (0.24), residues: 397 sheet: -1.32 (0.20), residues: 641 loop : -1.60 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP K 36 HIS 0.016 0.002 HIS K 102 PHE 0.028 0.003 PHE I 349 TYR 0.039 0.002 TYR J 550 ARG 0.011 0.001 ARG E 277 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 597) hydrogen bonds : angle 6.20100 ( 1623) SS BOND : bond 0.00921 ( 38) SS BOND : angle 1.74453 ( 76) covalent geometry : bond 0.00450 (18841) covalent geometry : angle 0.75974 (25570) *********************** 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 359 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 2.078 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: A 9 TYR cc_start: 0.9057 (m-80) cc_final: 0.8580 (m-80) REVERT: A 36 HIS cc_start: 0.7986 (m-70) cc_final: 0.7741 (m170) REVERT: A 65 MET cc_start: 0.9675 (ppp) cc_final: 0.9415 (ppp) REVERT: A 87 LYS cc_start: 0.9569 (ptpp) cc_final: 0.9275 (pttt) REVERT: A 118 MET cc_start: 0.8312 (mmp) cc_final: 0.7889 (tpp) REVERT: A 121 MET cc_start: 0.9266 (mmp) cc_final: 0.8855 (tpp) REVERT: A 246 LEU cc_start: 0.9601 (mt) cc_final: 0.9327 (pt) REVERT: A 338 ILE cc_start: 0.9454 (mm) cc_final: 0.9221 (pt) REVERT: A 395 MET cc_start: 0.9668 (ppp) cc_final: 0.9364 (ppp) REVERT: A 415 LEU cc_start: 0.9708 (mt) cc_final: 0.9417 (tp) REVERT: B 549 ARG cc_start: 0.9493 (mtt-85) cc_final: 0.9274 (mmm160) REVERT: B 553 ASP cc_start: 0.9238 (m-30) cc_final: 0.9033 (m-30) REVERT: C 11 MET cc_start: 0.9597 (mmp) cc_final: 0.9080 (mmp) REVERT: C 27 TYR cc_start: 0.8305 (t80) cc_final: 0.7818 (t80) REVERT: C 97 ASN cc_start: 0.9482 (t0) cc_final: 0.9173 (p0) REVERT: D 36 TYR cc_start: 0.8507 (m-80) cc_final: 0.7578 (m-80) REVERT: D 87 TYR cc_start: 0.9385 (m-80) cc_final: 0.8733 (m-80) REVERT: E 9 TYR cc_start: 0.9592 (m-10) cc_final: 0.8990 (m-80) REVERT: E 15 TRP cc_start: 0.8507 (m-90) cc_final: 0.8027 (m-90) REVERT: E 65 MET cc_start: 0.9232 (ppp) cc_final: 0.8959 (ppp) REVERT: E 74 MET cc_start: 0.9541 (ppp) cc_final: 0.9133 (ppp) REVERT: E 76 GLU cc_start: 0.9589 (mm-30) cc_final: 0.9268 (mm-30) REVERT: E 156 ASN cc_start: 0.9275 (t0) cc_final: 0.8984 (p0) REVERT: E 350 PHE cc_start: 0.9365 (m-10) cc_final: 0.8861 (m-80) REVERT: E 388 TRP cc_start: 0.8734 (t-100) cc_final: 0.8050 (t-100) REVERT: E 395 MET cc_start: 0.9698 (ppp) cc_final: 0.9239 (ppp) REVERT: E 437 MET cc_start: 0.9250 (mmt) cc_final: 0.8701 (tpt) REVERT: E 441 TRP cc_start: 0.9235 (m-10) cc_final: 0.8643 (m-90) REVERT: F 538 LYS cc_start: 0.9683 (mmpt) cc_final: 0.9437 (mmtm) REVERT: F 549 ARG cc_start: 0.9268 (mmm160) cc_final: 0.8818 (tpm170) REVERT: F 553 ASP cc_start: 0.9502 (m-30) cc_final: 0.8743 (m-30) REVERT: F 599 ILE cc_start: 0.9571 (mm) cc_final: 0.9220 (mm) REVERT: G 11 MET cc_start: 0.9531 (mmp) cc_final: 0.9230 (mmp) REVERT: G 27 TYR cc_start: 0.7308 (t80) cc_final: 0.5901 (t80) REVERT: G 28 GLU cc_start: 0.8770 (pm20) cc_final: 0.8216 (pm20) REVERT: G 51 LEU cc_start: 0.9544 (tp) cc_final: 0.9291 (tp) REVERT: G 69 MET cc_start: 0.9147 (pmm) cc_final: 0.8878 (pmm) REVERT: G 97 ASN cc_start: 0.9320 (t0) cc_final: 0.9088 (t0) REVERT: H 87 TYR cc_start: 0.9442 (m-80) cc_final: 0.8728 (m-80) REVERT: I 76 GLU cc_start: 0.9635 (mm-30) cc_final: 0.9355 (mm-30) REVERT: I 83 ASP cc_start: 0.9728 (t70) cc_final: 0.9521 (t0) REVERT: I 87 LYS cc_start: 0.9567 (ptpp) cc_final: 0.9295 (pttt) REVERT: I 156 ASN cc_start: 0.9296 (t0) cc_final: 0.9059 (p0) REVERT: I 239 ILE cc_start: 0.9339 (mm) cc_final: 0.9018 (mm) REVERT: I 316 GLU cc_start: 0.9475 (mm-30) cc_final: 0.9195 (mm-30) REVERT: I 343 PHE cc_start: 0.8327 (p90) cc_final: 0.8093 (p90) REVERT: I 395 MET cc_start: 0.9686 (ppp) cc_final: 0.9100 (ppp) REVERT: I 400 ILE cc_start: 0.9355 (mt) cc_final: 0.9111 (pt) REVERT: I 414 LEU cc_start: 0.9488 (mt) cc_final: 0.9151 (mt) REVERT: I 415 LEU cc_start: 0.9700 (mp) cc_final: 0.9145 (tp) REVERT: I 454 GLU cc_start: 0.9457 (mm-30) cc_final: 0.8460 (mp0) REVERT: J 548 GLU cc_start: 0.9476 (tt0) cc_final: 0.8985 (tm-30) REVERT: J 549 ARG cc_start: 0.9609 (mmm-85) cc_final: 0.9093 (mtm180) REVERT: J 551 LEU cc_start: 0.9884 (mt) cc_final: 0.9665 (pp) REVERT: K 11 MET cc_start: 0.9620 (mmp) cc_final: 0.9073 (mmp) REVERT: K 27 TYR cc_start: 0.7939 (t80) cc_final: 0.7581 (t80) REVERT: K 51 LEU cc_start: 0.9353 (tp) cc_final: 0.9061 (tp) REVERT: K 69 MET cc_start: 0.8996 (pmm) cc_final: 0.8780 (pmm) REVERT: K 97 ASN cc_start: 0.9525 (t0) cc_final: 0.9271 (p0) REVERT: L 87 TYR cc_start: 0.9276 (m-80) cc_final: 0.8973 (m-80) REVERT: L 89 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: L 97 PHE cc_start: 0.8590 (m-80) cc_final: 0.8213 (m-80) outliers start: 2 outliers final: 0 residues processed: 358 average time/residue: 0.2845 time to fit residues: 157.0544 Evaluate side-chains 286 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 76 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 31 optimal weight: 0.0370 chunk 82 optimal weight: 5.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- 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 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 ASN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.042979 restraints weight = 140566.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.044642 restraints weight = 88028.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.045845 restraints weight = 61955.802| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.7904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18879 Z= 0.125 Angle : 0.707 9.718 25646 Z= 0.372 Chirality : 0.047 0.209 2814 Planarity : 0.005 0.089 3281 Dihedral : 6.203 37.305 2530 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.27 % Favored : 92.64 % Rotamer: Outliers : 0.05 % Allowed : 0.69 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2297 helix: -0.47 (0.25), residues: 382 sheet: -1.09 (0.20), residues: 649 loop : -1.59 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 306 HIS 0.018 0.001 HIS C 102 PHE 0.026 0.002 PHE I 349 TYR 0.023 0.001 TYR F 550 ARG 0.009 0.001 ARG E 277 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 597) hydrogen bonds : angle 5.74879 ( 1623) SS BOND : bond 0.00296 ( 38) SS BOND : angle 1.56734 ( 76) covalent geometry : bond 0.00274 (18841) covalent geometry : angle 0.70305 (25570) *********************** 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 389 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 388 time to evaluate : 2.408 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: A 9 TYR cc_start: 0.8985 (m-80) cc_final: 0.8390 (m-80) REVERT: A 10 TYR cc_start: 0.9066 (t80) cc_final: 0.7530 (p90) REVERT: A 65 MET cc_start: 0.9705 (ppp) cc_final: 0.9487 (ppp) REVERT: A 83 ASP cc_start: 0.9709 (t70) cc_final: 0.9477 (t0) REVERT: A 87 LYS cc_start: 0.9540 (ptpp) cc_final: 0.9250 (pttt) REVERT: A 118 MET cc_start: 0.8289 (mmp) cc_final: 0.7733 (tpp) REVERT: A 121 MET cc_start: 0.9153 (mmp) cc_final: 0.8594 (tpp) REVERT: A 195 LEU cc_start: 0.9383 (mp) cc_final: 0.9113 (pt) REVERT: A 239 ILE cc_start: 0.9442 (mm) cc_final: 0.9136 (mm) REVERT: A 246 LEU cc_start: 0.9549 (mt) cc_final: 0.9274 (pt) REVERT: A 338 ILE cc_start: 0.9382 (mm) cc_final: 0.9117 (pt) REVERT: A 395 MET cc_start: 0.9596 (ppp) cc_final: 0.9298 (ppp) REVERT: A 415 LEU cc_start: 0.9728 (mt) cc_final: 0.9459 (tp) REVERT: B 609 LEU cc_start: 0.9404 (pt) cc_final: 0.9158 (pp) REVERT: C 11 MET cc_start: 0.9567 (mmp) cc_final: 0.9054 (mmp) REVERT: C 27 TYR cc_start: 0.7940 (t80) cc_final: 0.6568 (t80) REVERT: C 28 GLU cc_start: 0.8708 (pm20) cc_final: 0.8245 (pm20) REVERT: C 101 GLU cc_start: 0.9448 (tp30) cc_final: 0.9242 (tt0) REVERT: D 2 ILE cc_start: 0.7802 (tt) cc_final: 0.7568 (tp) REVERT: D 36 TYR cc_start: 0.8327 (m-80) cc_final: 0.7315 (m-80) REVERT: D 87 TYR cc_start: 0.9398 (m-80) cc_final: 0.8740 (m-80) REVERT: E 9 TYR cc_start: 0.9518 (m-10) cc_final: 0.9068 (m-80) REVERT: E 15 TRP cc_start: 0.8361 (m-90) cc_final: 0.7990 (m-90) REVERT: E 65 MET cc_start: 0.9201 (ppp) cc_final: 0.8960 (ppp) REVERT: E 74 MET cc_start: 0.9537 (ppp) cc_final: 0.9236 (ppp) REVERT: E 76 GLU cc_start: 0.9553 (mm-30) cc_final: 0.9241 (mm-30) REVERT: E 121 MET cc_start: 0.9233 (mmm) cc_final: 0.8806 (mmm) REVERT: E 147 ASP cc_start: 0.9234 (p0) cc_final: 0.8860 (m-30) REVERT: E 156 ASN cc_start: 0.9346 (t0) cc_final: 0.9061 (p0) REVERT: E 162 LEU cc_start: 0.9333 (tp) cc_final: 0.9007 (tp) REVERT: E 350 PHE cc_start: 0.9388 (m-10) cc_final: 0.8919 (m-80) REVERT: E 388 TRP cc_start: 0.8603 (t-100) cc_final: 0.7790 (t-100) REVERT: E 395 MET cc_start: 0.9660 (ppp) cc_final: 0.9336 (ppp) REVERT: E 437 MET cc_start: 0.9334 (mmt) cc_final: 0.8885 (tpt) REVERT: F 567 ILE cc_start: 0.9462 (mp) cc_final: 0.9169 (mm) REVERT: G 27 TYR cc_start: 0.7214 (t80) cc_final: 0.5841 (t80) REVERT: G 28 GLU cc_start: 0.8868 (pm20) cc_final: 0.8322 (pm20) REVERT: G 69 MET cc_start: 0.9045 (pmm) cc_final: 0.8805 (pmm) REVERT: G 97 ASN cc_start: 0.9266 (t0) cc_final: 0.9037 (t0) REVERT: G 101 GLU cc_start: 0.9691 (tp30) cc_final: 0.9403 (tt0) REVERT: H 87 TYR cc_start: 0.9453 (m-80) cc_final: 0.8765 (m-80) REVERT: I 76 GLU cc_start: 0.9590 (mm-30) cc_final: 0.9308 (mm-30) REVERT: I 87 LYS cc_start: 0.9565 (ptpp) cc_final: 0.9285 (pttt) REVERT: I 121 MET cc_start: 0.8777 (mmp) cc_final: 0.7831 (tpp) REVERT: I 156 ASN cc_start: 0.9304 (t0) cc_final: 0.9067 (p0) REVERT: I 343 PHE cc_start: 0.8446 (p90) cc_final: 0.8217 (p90) REVERT: I 395 MET cc_start: 0.9678 (ppp) cc_final: 0.9186 (ppp) REVERT: I 400 ILE cc_start: 0.9377 (mt) cc_final: 0.9137 (pt) REVERT: I 415 LEU cc_start: 0.9650 (mp) cc_final: 0.9129 (tp) REVERT: I 454 GLU cc_start: 0.9391 (mm-30) cc_final: 0.8425 (pm20) REVERT: J 548 GLU cc_start: 0.9446 (tt0) cc_final: 0.8940 (tm-30) REVERT: J 549 ARG cc_start: 0.9612 (mmm-85) cc_final: 0.9058 (mtm180) REVERT: J 551 LEU cc_start: 0.9864 (mt) cc_final: 0.9580 (pp) REVERT: J 607 TYR cc_start: 0.8714 (m-80) cc_final: 0.8343 (m-80) REVERT: K 11 MET cc_start: 0.9561 (mmp) cc_final: 0.8984 (mmp) REVERT: K 27 TYR cc_start: 0.8187 (t80) cc_final: 0.5954 (t80) REVERT: K 28 GLU cc_start: 0.9789 (mp0) cc_final: 0.9368 (pm20) REVERT: K 31 ASP cc_start: 0.9444 (m-30) cc_final: 0.9235 (t0) REVERT: K 51 LEU cc_start: 0.9264 (tp) cc_final: 0.8923 (tp) REVERT: K 69 MET cc_start: 0.8913 (pmm) cc_final: 0.8446 (pmm) REVERT: K 80 LEU cc_start: 0.9668 (tt) cc_final: 0.9383 (tt) REVERT: K 97 ASN cc_start: 0.9486 (t0) cc_final: 0.9244 (p0) REVERT: L 87 TYR cc_start: 0.9283 (m-80) cc_final: 0.8772 (m-80) outliers start: 1 outliers final: 0 residues processed: 389 average time/residue: 0.2981 time to fit residues: 177.1530 Evaluate side-chains 303 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 41 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** I 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.041233 restraints weight = 152026.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.042771 restraints weight = 95784.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.043911 restraints weight = 67684.293| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.8328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18879 Z= 0.200 Angle : 0.764 10.041 25646 Z= 0.407 Chirality : 0.047 0.260 2814 Planarity : 0.006 0.091 3281 Dihedral : 6.457 35.048 2530 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.66 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.17), residues: 2297 helix: -0.83 (0.24), residues: 391 sheet: -1.15 (0.21), residues: 599 loop : -1.50 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 15 HIS 0.013 0.001 HIS K 102 PHE 0.038 0.003 PHE I 349 TYR 0.038 0.002 TYR J 550 ARG 0.012 0.001 ARG F 549 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 597) hydrogen bonds : angle 6.15608 ( 1623) SS BOND : bond 0.00394 ( 38) SS BOND : angle 1.64597 ( 76) covalent geometry : bond 0.00426 (18841) covalent geometry : angle 0.76008 (25570) *********************** 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 361 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 2.383 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: A 9 TYR cc_start: 0.8945 (m-80) cc_final: 0.8442 (m-80) REVERT: A 49 PRO cc_start: 0.6932 (Cg_exo) cc_final: 0.6639 (Cg_endo) REVERT: A 65 MET cc_start: 0.9697 (ppp) cc_final: 0.9424 (ppp) REVERT: A 76 GLU cc_start: 0.9436 (mp0) cc_final: 0.9181 (pm20) REVERT: A 83 ASP cc_start: 0.9717 (t70) cc_final: 0.9450 (t0) REVERT: A 87 LYS cc_start: 0.9469 (ptpp) cc_final: 0.9158 (pttt) REVERT: A 118 MET cc_start: 0.8181 (mmp) cc_final: 0.7712 (tpp) REVERT: A 121 MET cc_start: 0.9119 (mmp) cc_final: 0.8514 (tpp) REVERT: A 195 LEU cc_start: 0.9440 (mp) cc_final: 0.9103 (pt) REVERT: A 246 LEU cc_start: 0.9589 (mt) cc_final: 0.9313 (pt) REVERT: A 338 ILE cc_start: 0.9411 (mm) cc_final: 0.9144 (pt) REVERT: A 344 ASN cc_start: 0.9008 (t0) cc_final: 0.8781 (t0) REVERT: A 395 MET cc_start: 0.9628 (ppp) cc_final: 0.9335 (ppp) REVERT: A 415 LEU cc_start: 0.9719 (mt) cc_final: 0.9464 (tp) REVERT: C 11 MET cc_start: 0.9596 (mmp) cc_final: 0.9040 (mmp) REVERT: C 27 TYR cc_start: 0.7777 (t80) cc_final: 0.6747 (t80) REVERT: C 28 GLU cc_start: 0.8639 (pm20) cc_final: 0.8396 (pm20) REVERT: C 51 LEU cc_start: 0.9376 (tp) cc_final: 0.9144 (tp) REVERT: C 86 ASP cc_start: 0.9230 (m-30) cc_final: 0.8945 (m-30) REVERT: C 100 ASP cc_start: 0.9625 (p0) cc_final: 0.9406 (p0) REVERT: C 110 ILE cc_start: 0.9698 (mm) cc_final: 0.9465 (mm) REVERT: D 2 ILE cc_start: 0.7982 (tt) cc_final: 0.7757 (tp) REVERT: D 36 TYR cc_start: 0.8554 (m-80) cc_final: 0.7678 (m-80) REVERT: D 87 TYR cc_start: 0.9356 (m-80) cc_final: 0.8644 (m-80) REVERT: E 9 TYR cc_start: 0.9559 (m-10) cc_final: 0.9029 (m-80) REVERT: E 15 TRP cc_start: 0.8433 (m-90) cc_final: 0.8013 (m-90) REVERT: E 65 MET cc_start: 0.9205 (ppp) cc_final: 0.8965 (ppp) REVERT: E 74 MET cc_start: 0.9554 (ppp) cc_final: 0.9185 (ppp) REVERT: E 76 GLU cc_start: 0.9584 (mm-30) cc_final: 0.9240 (mm-30) REVERT: E 121 MET cc_start: 0.9217 (mmm) cc_final: 0.8343 (mmm) REVERT: E 156 ASN cc_start: 0.9300 (t0) cc_final: 0.9006 (p0) REVERT: E 350 PHE cc_start: 0.9361 (m-10) cc_final: 0.8907 (m-80) REVERT: E 388 TRP cc_start: 0.8735 (t-100) cc_final: 0.8041 (t-100) REVERT: E 395 MET cc_start: 0.9690 (ppp) cc_final: 0.9341 (ppp) REVERT: E 437 MET cc_start: 0.9261 (mmt) cc_final: 0.8735 (tpt) REVERT: E 441 TRP cc_start: 0.9154 (m-10) cc_final: 0.8549 (m-90) REVERT: F 549 ARG cc_start: 0.9189 (mmm160) cc_final: 0.8860 (tpm170) REVERT: F 553 ASP cc_start: 0.9517 (m-30) cc_final: 0.8898 (m-30) REVERT: G 27 TYR cc_start: 0.7365 (t80) cc_final: 0.5916 (t80) REVERT: G 28 GLU cc_start: 0.8986 (pm20) cc_final: 0.8500 (pm20) REVERT: G 51 LEU cc_start: 0.9563 (tp) cc_final: 0.9311 (tp) REVERT: G 69 MET cc_start: 0.9206 (pmm) cc_final: 0.8936 (pmm) REVERT: G 82 LEU cc_start: 0.9385 (tp) cc_final: 0.9177 (tp) REVERT: G 97 ASN cc_start: 0.9293 (t0) cc_final: 0.9041 (t0) REVERT: H 87 TYR cc_start: 0.9438 (m-80) cc_final: 0.8583 (m-80) REVERT: I 76 GLU cc_start: 0.9578 (mm-30) cc_final: 0.9307 (mm-30) REVERT: I 83 ASP cc_start: 0.9712 (t70) cc_final: 0.9491 (t0) REVERT: I 87 LYS cc_start: 0.9548 (ptpp) cc_final: 0.9306 (pttt) REVERT: I 121 MET cc_start: 0.8949 (mmp) cc_final: 0.8131 (tpp) REVERT: I 156 ASN cc_start: 0.9372 (t0) cc_final: 0.9129 (p0) REVERT: I 164 ASN cc_start: 0.9056 (m110) cc_final: 0.8827 (m-40) REVERT: I 239 ILE cc_start: 0.9287 (mm) cc_final: 0.9078 (mm) REVERT: I 312 GLU cc_start: 0.9642 (mt-10) cc_final: 0.9281 (mm-30) REVERT: I 316 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9118 (mm-30) REVERT: I 343 PHE cc_start: 0.8502 (p90) cc_final: 0.8177 (p90) REVERT: I 388 TRP cc_start: 0.8565 (t-100) cc_final: 0.7548 (t-100) REVERT: I 395 MET cc_start: 0.9659 (ppp) cc_final: 0.9181 (ppp) REVERT: I 400 ILE cc_start: 0.9342 (mt) cc_final: 0.9088 (pt) REVERT: I 414 LEU cc_start: 0.9490 (mt) cc_final: 0.9266 (mt) REVERT: I 415 LEU cc_start: 0.9703 (mp) cc_final: 0.9172 (tp) REVERT: I 437 MET cc_start: 0.9047 (ttt) cc_final: 0.8702 (tpt) REVERT: I 454 GLU cc_start: 0.9489 (mm-30) cc_final: 0.8566 (pm20) REVERT: J 548 GLU cc_start: 0.9424 (tt0) cc_final: 0.8939 (tm-30) REVERT: J 549 ARG cc_start: 0.9603 (mmm-85) cc_final: 0.9080 (mtm180) REVERT: J 551 LEU cc_start: 0.9897 (mt) cc_final: 0.9631 (pp) REVERT: J 596 ASP cc_start: 0.9594 (t0) cc_final: 0.9277 (p0) REVERT: J 607 TYR cc_start: 0.8775 (m-80) cc_final: 0.8375 (m-80) REVERT: J 616 GLN cc_start: 0.9632 (tm-30) cc_final: 0.9421 (tm-30) REVERT: K 11 MET cc_start: 0.9594 (mmp) cc_final: 0.9013 (mmp) REVERT: K 27 TYR cc_start: 0.8188 (t80) cc_final: 0.7735 (t80) REVERT: K 51 LEU cc_start: 0.9274 (tp) cc_final: 0.8990 (tp) REVERT: K 97 ASN cc_start: 0.9461 (t0) cc_final: 0.9228 (p0) REVERT: L 86 TYR cc_start: 0.9561 (m-80) cc_final: 0.9351 (m-80) REVERT: L 87 TYR cc_start: 0.9319 (m-80) cc_final: 0.8840 (m-80) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.2902 time to fit residues: 160.9066 Evaluate side-chains 280 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 89 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 chunk 228 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 215 GLN ** 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 440 ASN ** I 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.050769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.041216 restraints weight = 148276.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.042789 restraints weight = 92872.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.043966 restraints weight = 65345.009| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.8574 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= 0.170 Angle : 0.742 10.584 25646 Z= 0.395 Chirality : 0.047 0.192 2814 Planarity : 0.006 0.092 3281 Dihedral : 6.383 36.083 2530 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.10 % Favored : 91.82 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2297 helix: -0.76 (0.25), residues: 376 sheet: -1.15 (0.21), residues: 612 loop : -1.46 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP F 560 HIS 0.012 0.001 HIS K 102 PHE 0.041 0.003 PHE I 349 TYR 0.034 0.002 TYR J 550 ARG 0.012 0.001 ARG F 549 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 597) hydrogen bonds : angle 6.08666 ( 1623) SS BOND : bond 0.00326 ( 38) SS BOND : angle 1.47073 ( 76) covalent geometry : bond 0.00367 (18841) covalent geometry : angle 0.73924 (25570) ********************** 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 357 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8899 (m-80) cc_final: 0.8407 (m-80) REVERT: A 10 TYR cc_start: 0.9167 (t80) cc_final: 0.8325 (t80) REVERT: A 49 PRO cc_start: 0.6933 (Cg_exo) cc_final: 0.6652 (Cg_endo) REVERT: A 65 MET cc_start: 0.9700 (ppp) cc_final: 0.9426 (ppp) REVERT: A 76 GLU cc_start: 0.9445 (mp0) cc_final: 0.9241 (pm20) REVERT: A 83 ASP cc_start: 0.9713 (t70) cc_final: 0.9468 (t0) REVERT: A 87 LYS cc_start: 0.9451 (ptpp) cc_final: 0.9110 (pttt) REVERT: A 118 MET cc_start: 0.8199 (mmp) cc_final: 0.7591 (tpp) REVERT: A 121 MET cc_start: 0.9112 (mmp) cc_final: 0.8405 (tpp) REVERT: A 195 LEU cc_start: 0.9416 (mp) cc_final: 0.9180 (pt) REVERT: A 246 LEU cc_start: 0.9597 (mt) cc_final: 0.9337 (pt) REVERT: A 338 ILE cc_start: 0.9339 (mm) cc_final: 0.9083 (pt) REVERT: A 395 MET cc_start: 0.9605 (ppp) cc_final: 0.9324 (ppp) REVERT: A 415 LEU cc_start: 0.9733 (mt) cc_final: 0.9468 (tp) REVERT: B 509 LEU cc_start: 0.9441 (pt) cc_final: 0.9230 (pt) REVERT: C 11 MET cc_start: 0.9607 (mmp) cc_final: 0.9064 (mmp) REVERT: C 27 TYR cc_start: 0.7755 (t80) cc_final: 0.6484 (t80) REVERT: C 28 GLU cc_start: 0.8757 (pm20) cc_final: 0.8433 (pm20) REVERT: C 86 ASP cc_start: 0.9138 (m-30) cc_final: 0.8916 (m-30) REVERT: C 97 ASN cc_start: 0.9325 (p0) cc_final: 0.9074 (p0) REVERT: C 100 ASN cc_start: 0.9328 (m110) cc_final: 0.9122 (m110) REVERT: C 110 ILE cc_start: 0.9686 (mm) cc_final: 0.9418 (mm) REVERT: D 17 GLU cc_start: 0.9726 (mt-10) cc_final: 0.9523 (mp0) REVERT: D 36 TYR cc_start: 0.8468 (m-80) cc_final: 0.7588 (m-80) REVERT: D 87 TYR cc_start: 0.9337 (m-80) cc_final: 0.8613 (m-80) REVERT: E 9 TYR cc_start: 0.9571 (m-10) cc_final: 0.9170 (m-80) REVERT: E 15 TRP cc_start: 0.8436 (m-90) cc_final: 0.8048 (m-90) REVERT: E 65 MET cc_start: 0.9206 (ppp) cc_final: 0.8958 (ppp) REVERT: E 74 MET cc_start: 0.9547 (ppp) cc_final: 0.9168 (ppp) REVERT: E 76 GLU cc_start: 0.9568 (mm-30) cc_final: 0.9211 (mm-30) REVERT: E 121 MET cc_start: 0.9231 (mmm) cc_final: 0.8557 (mmm) REVERT: E 147 ASP cc_start: 0.9371 (p0) cc_final: 0.8824 (m-30) REVERT: E 156 ASN cc_start: 0.9305 (t0) cc_final: 0.9028 (p0) REVERT: E 246 LEU cc_start: 0.9613 (mt) cc_final: 0.9171 (pt) REVERT: E 350 PHE cc_start: 0.9366 (m-10) cc_final: 0.8923 (m-80) REVERT: E 388 TRP cc_start: 0.8643 (t-100) cc_final: 0.8040 (t-100) REVERT: E 395 MET cc_start: 0.9704 (ppp) cc_final: 0.9356 (ppp) REVERT: E 437 MET cc_start: 0.9289 (mmt) cc_final: 0.8742 (tpt) REVERT: E 441 TRP cc_start: 0.9139 (m-10) cc_final: 0.8513 (m-90) REVERT: F 549 ARG cc_start: 0.9201 (mmm160) cc_final: 0.8857 (tpm170) REVERT: F 553 ASP cc_start: 0.9540 (m-30) cc_final: 0.8778 (m-30) REVERT: F 567 ILE cc_start: 0.9498 (mp) cc_final: 0.9212 (mm) REVERT: G 27 TYR cc_start: 0.7356 (t80) cc_final: 0.5890 (t80) REVERT: G 28 GLU cc_start: 0.9047 (pm20) cc_final: 0.8615 (pm20) REVERT: G 51 LEU cc_start: 0.9563 (tp) cc_final: 0.9327 (tp) REVERT: G 69 MET cc_start: 0.9122 (pmm) cc_final: 0.8838 (pmm) REVERT: G 97 ASN cc_start: 0.9269 (t0) cc_final: 0.9050 (t0) REVERT: H 87 TYR cc_start: 0.9474 (m-80) cc_final: 0.8746 (m-80) REVERT: I 74 MET cc_start: 0.9778 (ppp) cc_final: 0.9404 (ppp) REVERT: I 76 GLU cc_start: 0.9569 (mm-30) cc_final: 0.9247 (mm-30) REVERT: I 83 ASP cc_start: 0.9706 (t70) cc_final: 0.9488 (t0) REVERT: I 87 LYS cc_start: 0.9553 (ptpp) cc_final: 0.9318 (pttt) REVERT: I 121 MET cc_start: 0.8914 (mmp) cc_final: 0.7767 (tpp) REVERT: I 142 LEU cc_start: 0.9386 (mt) cc_final: 0.9074 (mt) REVERT: I 156 ASN cc_start: 0.9362 (t0) cc_final: 0.9118 (p0) REVERT: I 164 ASN cc_start: 0.9061 (m110) cc_final: 0.8819 (m-40) REVERT: I 239 ILE cc_start: 0.9234 (mm) cc_final: 0.8991 (mm) REVERT: I 312 GLU cc_start: 0.9657 (mt-10) cc_final: 0.9437 (mt-10) REVERT: I 316 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9143 (mm-30) REVERT: I 343 PHE cc_start: 0.8378 (p90) cc_final: 0.8153 (p90) REVERT: I 388 TRP cc_start: 0.8458 (t-100) cc_final: 0.7595 (t-100) REVERT: I 395 MET cc_start: 0.9661 (ppp) cc_final: 0.9201 (ppp) REVERT: I 400 ILE cc_start: 0.9370 (mt) cc_final: 0.9132 (pt) REVERT: I 414 LEU cc_start: 0.9502 (mt) cc_final: 0.9281 (mt) REVERT: I 415 LEU cc_start: 0.9693 (mp) cc_final: 0.9191 (tp) REVERT: I 437 MET cc_start: 0.9167 (ttt) cc_final: 0.8278 (tpt) REVERT: I 441 TRP cc_start: 0.8833 (m-10) cc_final: 0.7948 (m100) REVERT: I 454 GLU cc_start: 0.9454 (mm-30) cc_final: 0.8553 (pm20) REVERT: J 548 GLU cc_start: 0.9332 (tt0) cc_final: 0.8872 (tm-30) REVERT: J 549 ARG cc_start: 0.9606 (mmm-85) cc_final: 0.9066 (mtm180) REVERT: J 551 LEU cc_start: 0.9901 (mt) cc_final: 0.9647 (pp) REVERT: J 596 ASP cc_start: 0.9610 (t0) cc_final: 0.9382 (p0) REVERT: J 607 TYR cc_start: 0.8836 (m-80) cc_final: 0.8410 (m-80) REVERT: J 616 GLN cc_start: 0.9671 (tm-30) cc_final: 0.9452 (tm-30) REVERT: K 11 MET cc_start: 0.9609 (mmp) cc_final: 0.9082 (mmp) REVERT: K 23 ARG cc_start: 0.9579 (ttm110) cc_final: 0.9318 (ptp90) REVERT: K 39 LEU cc_start: 0.9841 (pp) cc_final: 0.9575 (tp) REVERT: K 51 LEU cc_start: 0.9322 (tp) cc_final: 0.9017 (tp) REVERT: K 97 ASN cc_start: 0.9447 (t0) cc_final: 0.9243 (p0) REVERT: L 86 TYR cc_start: 0.9572 (m-80) cc_final: 0.9327 (m-80) REVERT: L 87 TYR cc_start: 0.9349 (m-80) cc_final: 0.8843 (m-80) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.2790 time to fit residues: 154.3295 Evaluate side-chains 281 residues out of total 2039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 224 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 215 GLN ** 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 409 ASN E 440 ASN I 423 ASN ** I 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.051867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.041974 restraints weight = 145400.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.043592 restraints weight = 91706.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.044753 restraints weight = 64745.076| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.8702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18879 Z= 0.133 Angle : 0.715 10.444 25646 Z= 0.378 Chirality : 0.046 0.186 2814 Planarity : 0.005 0.084 3281 Dihedral : 6.115 37.108 2530 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.97 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.17), residues: 2297 helix: -0.67 (0.25), residues: 376 sheet: -0.97 (0.20), residues: 653 loop : -1.48 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 35 HIS 0.011 0.001 HIS K 102 PHE 0.039 0.002 PHE I 349 TYR 0.027 0.001 TYR L 36 ARG 0.010 0.001 ARG F 549 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 597) hydrogen bonds : angle 5.86137 ( 1623) SS BOND : bond 0.00318 ( 38) SS BOND : angle 1.40481 ( 76) covalent geometry : bond 0.00295 (18841) covalent geometry : angle 0.71184 (25570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5710.23 seconds wall clock time: 100 minutes 30.78 seconds (6030.78 seconds total)