Starting phenix.real_space_refine on Sun Mar 17 18:07:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sal_40273/03_2024/8sal_40273_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sal_40273/03_2024/8sal_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sal_40273/03_2024/8sal_40273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sal_40273/03_2024/8sal_40273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sal_40273/03_2024/8sal_40273_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sal_40273/03_2024/8sal_40273_neut.pdb" } 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 Residue "A ASP 418": "OD1" <-> "OD2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 418": "OD1" <-> "OD2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 60": "OD1" <-> "OD2" Residue "I TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 418": "OD1" <-> "OD2" Residue "L ASP 60": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.95, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 6.54 Conformation dependent library (CDL) restraints added in 3.4 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: 2.42 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: 7.08 Time building geometry restraints manager: 7.26 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: 97.27 - 104.63: 322 104.63 - 111.99: 8996 111.99 - 119.36: 6564 119.36 - 126.72: 9318 126.72 - 134.08: 370 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 2.440 nonbonded pdb=" OE1 GLU I 303 " pdb=" OG SER I 371 " model vdw 2.096 2.440 nonbonded pdb=" OE1 GLU E 303 " pdb=" OG SER E 371 " model vdw 2.097 2.440 nonbonded pdb=" OE1 GLU A 303 " pdb=" OG SER A 371 " model vdw 2.098 2.440 nonbonded pdb=" O ASN E 440 " pdb=" OG SER E 443 " model vdw 2.111 2.440 ... (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 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.860 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 49.750 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.100 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.640 ------------------------------------------------------------------------------- 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 18841 Z= 0.328 Angle : 0.889 14.235 25570 Z= 0.498 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 678 time to evaluate : 2.161 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: 0.3383 time to fit residues: 328.1886 Evaluate side-chains 440 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 2.003 ------------------------------------------------------------------------------- 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: 20.0000 chunk 174 optimal weight: 0.1980 chunk 96 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 208 optimal weight: 30.0000 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** 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 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN ** C 64 GLN ** 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 E 318 GLN H 38 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 298 HIS I 305 GLN I 423 ASN K 64 GLN L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18841 Z= 0.232 Angle : 0.720 7.865 25570 Z= 0.388 Chirality : 0.047 0.223 2814 Planarity : 0.005 0.099 3281 Dihedral : 6.803 35.388 2530 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.31 % Favored : 93.56 % Rotamer: Outliers : 0.49 % Allowed : 4.02 % Favored : 95.49 % 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: -1.94 (0.17), residues: 2297 helix: -0.51 (0.24), residues: 437 sheet: -1.29 (0.21), residues: 593 loop : -1.55 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 441 HIS 0.007 0.001 HIS I 185 PHE 0.031 0.002 PHE A 179 TYR 0.020 0.002 TYR C 100 ARG 0.013 0.001 ARG C 44 *********************** 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 515 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 505 time to evaluate : 2.203 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: A 10 TYR cc_start: 0.8799 (t80) cc_final: 0.7624 (p90) REVERT: A 36 HIS cc_start: 0.7282 (m-70) cc_final: 0.7026 (m170) REVERT: A 65 MET cc_start: 0.9534 (ppp) cc_final: 0.9041 (ppp) REVERT: A 74 MET cc_start: 0.9705 (tmm) cc_final: 0.9426 (tmm) REVERT: A 162 LEU cc_start: 0.9529 (mt) cc_final: 0.9219 (mt) REVERT: A 357 LEU cc_start: 0.9703 (mt) cc_final: 0.9427 (mt) REVERT: A 377 LEU cc_start: 0.9396 (mt) cc_final: 0.9075 (tp) REVERT: A 389 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8608 (tm-30) REVERT: A 395 MET cc_start: 0.9527 (ppp) cc_final: 0.9263 (ppp) REVERT: A 400 ILE cc_start: 0.9240 (mt) cc_final: 0.8972 (pt) REVERT: A 414 LEU cc_start: 0.9771 (mt) cc_final: 0.9554 (mt) REVERT: A 415 LEU cc_start: 0.9572 (mt) cc_final: 0.9283 (tp) REVERT: A 441 TRP cc_start: 0.9156 (m-10) cc_final: 0.8840 (m-90) REVERT: A 452 LYS cc_start: 0.9379 (pttt) cc_final: 0.9067 (ptmm) REVERT: B 548 GLU cc_start: 0.9596 (tt0) cc_final: 0.9386 (tt0) REVERT: B 549 ARG cc_start: 0.9714 (mtp180) cc_final: 0.9492 (mtp180) REVERT: B 560 TRP cc_start: 0.8392 (m-90) cc_final: 0.7181 (m-90) REVERT: B 587 TRP cc_start: 0.8939 (m100) cc_final: 0.8614 (m100) REVERT: B 602 TYR cc_start: 0.9692 (m-80) cc_final: 0.9482 (m-80) REVERT: B 607 TYR cc_start: 0.8503 (m-10) cc_final: 0.8284 (m-10) REVERT: C 27 TYR cc_start: 0.7500 (t80) cc_final: 0.6935 (t80) REVERT: C 39 LEU cc_start: 0.9727 (tt) cc_final: 0.9512 (mm) REVERT: C 48 MET cc_start: 0.9438 (mmp) cc_final: 0.9154 (mmm) REVERT: C 97 ASN cc_start: 0.9104 (t0) cc_final: 0.8789 (p0) REVERT: D 38 GLN cc_start: 0.9684 (OUTLIER) cc_final: 0.9355 (pp30) REVERT: D 60 ASP cc_start: 0.9514 (p0) cc_final: 0.9208 (t0) REVERT: D 62 PHE cc_start: 0.9241 (m-10) cc_final: 0.8977 (m-80) REVERT: D 87 TYR cc_start: 0.9378 (m-80) cc_final: 0.8948 (m-80) REVERT: E 65 MET cc_start: 0.9283 (ppp) cc_final: 0.8883 (ppp) REVERT: E 70 MET cc_start: 0.9641 (ppp) cc_final: 0.9427 (ppp) REVERT: E 74 MET cc_start: 0.9534 (ppp) cc_final: 0.9062 (ppp) REVERT: E 76 GLU cc_start: 0.9628 (mm-30) cc_final: 0.9413 (mm-30) REVERT: E 121 MET cc_start: 0.9151 (mmp) cc_final: 0.8812 (mmp) REVERT: E 156 ASN cc_start: 0.9124 (t0) cc_final: 0.8910 (p0) REVERT: E 162 LEU cc_start: 0.9414 (mt) cc_final: 0.9099 (mt) REVERT: E 239 ILE cc_start: 0.9603 (mm) cc_final: 0.9229 (mm) REVERT: E 316 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8752 (mm-30) REVERT: E 328 TYR cc_start: 0.8500 (m-80) cc_final: 0.8207 (m-10) REVERT: E 350 PHE cc_start: 0.9291 (m-80) cc_final: 0.8791 (m-80) REVERT: E 395 MET cc_start: 0.9429 (ppp) cc_final: 0.9047 (ppp) REVERT: E 400 ILE cc_start: 0.9340 (mt) cc_final: 0.9052 (pt) REVERT: E 437 MET cc_start: 0.9303 (mmt) cc_final: 0.8360 (tpp) REVERT: E 441 TRP cc_start: 0.9451 (m-10) cc_final: 0.8634 (m-90) REVERT: E 445 LEU cc_start: 0.9520 (mm) cc_final: 0.9310 (mm) REVERT: F 548 GLU cc_start: 0.9515 (pt0) cc_final: 0.9311 (pp20) REVERT: F 565 LYS cc_start: 0.9368 (mmtp) cc_final: 0.9132 (ptpp) REVERT: F 566 LEU cc_start: 0.8753 (mt) cc_final: 0.8353 (tt) REVERT: F 587 TRP cc_start: 0.8638 (m100) cc_final: 0.8203 (m100) REVERT: F 603 THR cc_start: 0.9691 (m) cc_final: 0.8855 (m) REVERT: G 27 TYR cc_start: 0.7335 (t80) cc_final: 0.5821 (t80) REVERT: G 28 GLU cc_start: 0.9743 (mp0) cc_final: 0.9345 (tp30) REVERT: G 80 LEU cc_start: 0.9721 (tp) cc_final: 0.9484 (tp) REVERT: G 97 ASN cc_start: 0.9211 (t0) cc_final: 0.8677 (p0) REVERT: H 36 TYR cc_start: 0.9153 (m-80) cc_final: 0.8765 (m-80) REVERT: H 62 PHE cc_start: 0.9282 (m-10) cc_final: 0.8899 (m-80) REVERT: H 87 TYR cc_start: 0.9456 (m-80) cc_final: 0.9035 (m-80) REVERT: I 23 PHE cc_start: 0.8956 (p90) cc_final: 0.8500 (p90) REVERT: I 65 MET cc_start: 0.9289 (ppp) cc_final: 0.8814 (ppp) REVERT: I 76 GLU cc_start: 0.9684 (mm-30) cc_final: 0.9481 (mm-30) REVERT: I 156 ASN cc_start: 0.9094 (t0) cc_final: 0.8835 (p0) REVERT: I 162 LEU cc_start: 0.9611 (mt) cc_final: 0.9340 (mt) REVERT: I 298 HIS cc_start: 0.8622 (m90) cc_final: 0.8159 (m-70) REVERT: I 328 TYR cc_start: 0.9048 (m-80) cc_final: 0.8818 (m-10) REVERT: I 343 PHE cc_start: 0.8748 (p90) cc_final: 0.8028 (p90) REVERT: I 350 PHE cc_start: 0.9103 (m-80) cc_final: 0.8422 (m-80) REVERT: I 395 MET cc_start: 0.9395 (ppp) cc_final: 0.9040 (ppp) REVERT: I 414 LEU cc_start: 0.9566 (mt) cc_final: 0.9221 (mt) REVERT: I 415 LEU cc_start: 0.9529 (mt) cc_final: 0.9216 (tp) REVERT: I 437 MET cc_start: 0.8850 (mmp) cc_final: 0.8595 (tpt) REVERT: I 454 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8034 (mp0) REVERT: J 545 LEU cc_start: 0.9746 (mm) cc_final: 0.9468 (mm) REVERT: J 547 VAL cc_start: 0.9623 (t) cc_final: 0.9385 (p) REVERT: J 548 GLU cc_start: 0.9628 (tt0) cc_final: 0.9325 (pt0) REVERT: J 599 ILE cc_start: 0.9289 (pt) cc_final: 0.8609 (pt) REVERT: J 606 ILE cc_start: 0.8235 (pt) cc_final: 0.7961 (pt) REVERT: K 27 TYR cc_start: 0.7382 (t80) cc_final: 0.6497 (t80) REVERT: K 28 GLU cc_start: 0.9765 (mp0) cc_final: 0.9515 (pm20) REVERT: K 39 LEU cc_start: 0.9716 (tt) cc_final: 0.9405 (mm) REVERT: K 97 ASN cc_start: 0.9085 (t0) cc_final: 0.8797 (p0) REVERT: L 62 PHE cc_start: 0.9221 (m-10) cc_final: 0.8916 (m-80) REVERT: L 87 TYR cc_start: 0.9324 (m-80) cc_final: 0.8988 (m-80) outliers start: 10 outliers final: 0 residues processed: 515 average time/residue: 0.3149 time to fit residues: 238.9007 Evaluate side-chains 361 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 173 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 226 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN F 539 GLN G 64 GLN H 38 GLN I 73 GLN I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 271 ASN I 409 ASN ** I 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18841 Z= 0.188 Angle : 0.669 8.389 25570 Z= 0.359 Chirality : 0.046 0.194 2814 Planarity : 0.005 0.058 3281 Dihedral : 6.380 34.940 2530 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.01 % Favored : 92.86 % Rotamer: Outliers : 0.15 % Allowed : 3.73 % Favored : 96.13 % 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: -1.80 (0.17), residues: 2297 helix: -0.30 (0.25), residues: 431 sheet: -1.11 (0.21), residues: 641 loop : -1.55 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 560 HIS 0.006 0.001 HIS E 75 PHE 0.032 0.002 PHE I 430 TYR 0.023 0.002 TYR F 607 ARG 0.006 0.001 ARG F 549 *********************** 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 459 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 456 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8829 (t80) cc_final: 0.7459 (p90) REVERT: A 36 HIS cc_start: 0.7416 (m-70) cc_final: 0.7123 (m170) REVERT: A 65 MET cc_start: 0.9535 (ppp) cc_final: 0.9226 (ppp) REVERT: A 66 TRP cc_start: 0.9362 (m100) cc_final: 0.9095 (m100) REVERT: A 74 MET cc_start: 0.9695 (tmm) cc_final: 0.9328 (tmm) REVERT: A 121 MET cc_start: 0.9101 (mmp) cc_final: 0.8716 (tpp) REVERT: A 162 LEU cc_start: 0.9390 (mt) cc_final: 0.9135 (mt) REVERT: A 239 ILE cc_start: 0.9555 (mm) cc_final: 0.9137 (mm) REVERT: A 316 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8921 (mm-30) REVERT: A 348 GLU cc_start: 0.9553 (mm-30) cc_final: 0.8812 (mm-30) REVERT: A 357 LEU cc_start: 0.9557 (mt) cc_final: 0.9348 (mt) REVERT: A 377 LEU cc_start: 0.9303 (mt) cc_final: 0.8983 (tp) REVERT: A 388 TRP cc_start: 0.8425 (t-100) cc_final: 0.7584 (t-100) REVERT: A 395 MET cc_start: 0.9566 (ppp) cc_final: 0.9352 (ppp) REVERT: A 400 ILE cc_start: 0.9392 (mt) cc_final: 0.8702 (pt) REVERT: A 414 LEU cc_start: 0.9728 (mt) cc_final: 0.9523 (mt) REVERT: A 415 LEU cc_start: 0.9529 (mt) cc_final: 0.9252 (tp) REVERT: A 437 MET cc_start: 0.8407 (tpt) cc_final: 0.8183 (tpt) REVERT: A 440 ASN cc_start: 0.9523 (p0) cc_final: 0.9239 (p0) REVERT: A 441 TRP cc_start: 0.9253 (m-10) cc_final: 0.8859 (m-90) REVERT: B 548 GLU cc_start: 0.9540 (tt0) cc_final: 0.9241 (tt0) REVERT: B 549 ARG cc_start: 0.9708 (mtp180) cc_final: 0.9096 (mmm-85) REVERT: B 560 TRP cc_start: 0.8154 (m-10) cc_final: 0.7434 (m-90) REVERT: B 599 ILE cc_start: 0.9436 (pt) cc_final: 0.8927 (pt) REVERT: B 606 ILE cc_start: 0.8183 (pt) cc_final: 0.7945 (pt) REVERT: B 607 TYR cc_start: 0.8547 (m-10) cc_final: 0.8320 (m-10) REVERT: B 614 GLN cc_start: 0.9642 (tp40) cc_final: 0.9368 (mm-40) REVERT: C 11 MET cc_start: 0.9461 (mmp) cc_final: 0.9115 (mmp) REVERT: C 27 TYR cc_start: 0.7879 (t80) cc_final: 0.6626 (t80) REVERT: C 28 GLU cc_start: 0.9781 (mp0) cc_final: 0.9266 (tp30) REVERT: C 48 MET cc_start: 0.9423 (mmp) cc_final: 0.9111 (mmm) REVERT: C 97 ASN cc_start: 0.9434 (t0) cc_final: 0.9090 (p0) REVERT: D 87 TYR cc_start: 0.9402 (m-80) cc_final: 0.8968 (m-80) REVERT: E 65 MET cc_start: 0.9042 (ppp) cc_final: 0.8770 (ppp) REVERT: E 74 MET cc_start: 0.9564 (ppp) cc_final: 0.9067 (ppp) REVERT: E 118 MET cc_start: 0.8421 (mmp) cc_final: 0.8174 (mmp) REVERT: E 121 MET cc_start: 0.9210 (mmp) cc_final: 0.8629 (mmm) REVERT: E 156 ASN cc_start: 0.9107 (t0) cc_final: 0.8892 (p0) REVERT: E 162 LEU cc_start: 0.9307 (mt) cc_final: 0.9020 (mt) REVERT: E 316 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8563 (mt-10) REVERT: E 350 PHE cc_start: 0.9238 (m-80) cc_final: 0.8771 (m-80) REVERT: E 395 MET cc_start: 0.9531 (ppp) cc_final: 0.9199 (ppp) REVERT: E 437 MET cc_start: 0.9321 (mmt) cc_final: 0.8568 (tpt) REVERT: E 441 TRP cc_start: 0.9488 (m-10) cc_final: 0.8967 (m-90) REVERT: F 553 ASP cc_start: 0.9299 (m-30) cc_final: 0.9042 (m-30) REVERT: F 554 GLN cc_start: 0.9533 (mm-40) cc_final: 0.9235 (mm110) REVERT: F 555 GLN cc_start: 0.9569 (tp40) cc_final: 0.9290 (tm-30) REVERT: F 559 ILE cc_start: 0.9063 (mt) cc_final: 0.8697 (mt) REVERT: F 566 LEU cc_start: 0.8971 (mt) cc_final: 0.8585 (tt) REVERT: F 587 TRP cc_start: 0.8854 (m100) cc_final: 0.8366 (m100) REVERT: G 27 TYR cc_start: 0.7862 (t80) cc_final: 0.7255 (t80) REVERT: G 28 GLU cc_start: 0.9688 (mp0) cc_final: 0.9430 (tp30) REVERT: G 39 LEU cc_start: 0.9709 (tt) cc_final: 0.9401 (mm) REVERT: G 80 LEU cc_start: 0.9733 (tp) cc_final: 0.9499 (tp) REVERT: G 82 LEU cc_start: 0.9358 (tp) cc_final: 0.9089 (tp) REVERT: G 93 THR cc_start: 0.6702 (m) cc_final: 0.6129 (t) REVERT: G 97 ASN cc_start: 0.9213 (t0) cc_final: 0.8644 (p0) REVERT: H 36 TYR cc_start: 0.9198 (m-80) cc_final: 0.8873 (m-80) REVERT: H 87 TYR cc_start: 0.9463 (m-80) cc_final: 0.9086 (m-80) REVERT: I 121 MET cc_start: 0.8799 (mmp) cc_final: 0.7982 (tpp) REVERT: I 156 ASN cc_start: 0.9095 (t0) cc_final: 0.8836 (p0) REVERT: I 239 ILE cc_start: 0.9445 (mm) cc_final: 0.9062 (mm) REVERT: I 298 HIS cc_start: 0.8615 (m90) cc_final: 0.8159 (m-70) REVERT: I 316 GLU cc_start: 0.9348 (mm-30) cc_final: 0.9075 (mm-30) REVERT: I 350 PHE cc_start: 0.9097 (m-80) cc_final: 0.8744 (m-80) REVERT: I 395 MET cc_start: 0.9500 (ppp) cc_final: 0.9042 (ppp) REVERT: I 400 ILE cc_start: 0.9335 (mt) cc_final: 0.9109 (pt) REVERT: I 452 LYS cc_start: 0.9347 (pttt) cc_final: 0.8990 (ptmm) REVERT: I 454 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8334 (mm-30) REVERT: J 548 GLU cc_start: 0.9599 (tt0) cc_final: 0.9212 (mt-10) REVERT: J 549 ARG cc_start: 0.9684 (mtp180) cc_final: 0.9472 (mmm-85) REVERT: J 553 ASP cc_start: 0.9033 (m-30) cc_final: 0.8718 (m-30) REVERT: J 559 ILE cc_start: 0.9225 (mt) cc_final: 0.8909 (mt) REVERT: J 599 ILE cc_start: 0.9182 (pt) cc_final: 0.8790 (pt) REVERT: K 27 TYR cc_start: 0.7452 (t80) cc_final: 0.6561 (t80) REVERT: K 28 GLU cc_start: 0.9794 (mp0) cc_final: 0.9305 (tp30) REVERT: K 51 LEU cc_start: 0.9360 (tp) cc_final: 0.9146 (tp) REVERT: K 97 ASN cc_start: 0.9219 (t0) cc_final: 0.8921 (p0) REVERT: L 87 TYR cc_start: 0.9341 (m-80) cc_final: 0.8978 (m-80) outliers start: 3 outliers final: 0 residues processed: 459 average time/residue: 0.3110 time to fit residues: 213.2755 Evaluate side-chains 334 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 209 optimal weight: 8.9990 chunk 222 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 571 ASN F 614 GLN F 615 ASN F 617 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 HIS I 127 ASN ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 383 GLN ** I 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 614 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 18841 Z= 0.379 Angle : 0.843 9.819 25570 Z= 0.455 Chirality : 0.048 0.213 2814 Planarity : 0.006 0.070 3281 Dihedral : 7.079 34.847 2530 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 31.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.66 % Favored : 91.12 % Rotamer: Outliers : 0.25 % Allowed : 4.81 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.11 (0.17), residues: 2297 helix: -1.01 (0.23), residues: 399 sheet: -1.24 (0.21), residues: 587 loop : -1.60 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 5 HIS 0.009 0.002 HIS A 341 PHE 0.028 0.004 PHE I 179 TYR 0.028 0.003 TYR G 100 ARG 0.013 0.001 ARG D 39 *********************** 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 381 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 376 time to evaluate : 2.204 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: A 9 TYR cc_start: 0.9255 (m-10) cc_final: 0.9011 (m-80) REVERT: A 65 MET cc_start: 0.9668 (ppp) cc_final: 0.9242 (ppp) REVERT: A 74 MET cc_start: 0.9724 (tmm) cc_final: 0.9486 (tmm) REVERT: A 118 MET cc_start: 0.8193 (mmp) cc_final: 0.7740 (mmp) REVERT: A 348 GLU cc_start: 0.9588 (mm-30) cc_final: 0.9219 (mm-30) REVERT: A 377 LEU cc_start: 0.9348 (mt) cc_final: 0.9060 (tp) REVERT: A 395 MET cc_start: 0.9645 (ppp) cc_final: 0.9427 (ppp) REVERT: A 415 LEU cc_start: 0.9660 (mt) cc_final: 0.9349 (tp) REVERT: A 437 MET cc_start: 0.8508 (tpt) cc_final: 0.8293 (tpt) REVERT: A 441 TRP cc_start: 0.9379 (m-10) cc_final: 0.9123 (m-90) REVERT: B 548 GLU cc_start: 0.9376 (tt0) cc_final: 0.9085 (tt0) REVERT: B 549 ARG cc_start: 0.9613 (mtp180) cc_final: 0.9243 (mmm-85) REVERT: B 606 ILE cc_start: 0.8557 (pt) cc_final: 0.8356 (pt) REVERT: B 607 TYR cc_start: 0.8201 (m-10) cc_final: 0.8000 (m-10) REVERT: C 11 MET cc_start: 0.9546 (mmp) cc_final: 0.9151 (mmp) REVERT: C 27 TYR cc_start: 0.7681 (t80) cc_final: 0.5189 (t80) REVERT: C 28 GLU cc_start: 0.9686 (mp0) cc_final: 0.9167 (pm20) REVERT: C 31 ASP cc_start: 0.9336 (t0) cc_final: 0.9088 (t0) REVERT: C 48 MET cc_start: 0.9444 (mmp) cc_final: 0.9221 (mmm) REVERT: C 82 LEU cc_start: 0.9096 (tp) cc_final: 0.8858 (tp) REVERT: C 97 ASN cc_start: 0.9263 (t0) cc_final: 0.8854 (p0) REVERT: D 87 TYR cc_start: 0.9391 (m-80) cc_final: 0.8774 (m-80) REVERT: E 9 TYR cc_start: 0.9239 (m-10) cc_final: 0.8491 (m-80) REVERT: E 15 TRP cc_start: 0.8656 (m-90) cc_final: 0.8211 (m-90) REVERT: E 65 MET cc_start: 0.9138 (ppp) cc_final: 0.8872 (ppp) REVERT: E 156 ASN cc_start: 0.9175 (t0) cc_final: 0.8948 (p0) REVERT: E 395 MET cc_start: 0.9621 (ppp) cc_final: 0.9268 (ppp) REVERT: E 437 MET cc_start: 0.9133 (mmt) cc_final: 0.8914 (tpt) REVERT: F 566 LEU cc_start: 0.9431 (mt) cc_final: 0.8977 (tt) REVERT: G 11 MET cc_start: 0.9578 (mmp) cc_final: 0.9210 (mmp) REVERT: G 18 MET cc_start: 0.9707 (tmm) cc_final: 0.9477 (tmm) REVERT: G 82 LEU cc_start: 0.9330 (tp) cc_final: 0.9126 (tp) REVERT: H 36 TYR cc_start: 0.9321 (m-80) cc_final: 0.9092 (m-80) REVERT: H 87 TYR cc_start: 0.9413 (m-80) cc_final: 0.8848 (m-80) REVERT: I 15 TRP cc_start: 0.8799 (m-10) cc_final: 0.8521 (m-10) REVERT: I 156 ASN cc_start: 0.9279 (t0) cc_final: 0.9026 (p0) REVERT: I 162 LEU cc_start: 0.8538 (tp) cc_final: 0.8214 (tp) REVERT: I 395 MET cc_start: 0.9697 (ppp) cc_final: 0.9330 (ppp) REVERT: I 400 ILE cc_start: 0.9289 (mt) cc_final: 0.9033 (pt) REVERT: I 454 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8069 (mp0) REVERT: J 548 GLU cc_start: 0.9512 (tt0) cc_final: 0.9177 (mt-10) REVERT: J 549 ARG cc_start: 0.9654 (mtp180) cc_final: 0.9353 (mtp180) REVERT: K 27 TYR cc_start: 0.7937 (t80) cc_final: 0.5734 (t80) REVERT: K 28 GLU cc_start: 0.9681 (mp0) cc_final: 0.9066 (pm20) REVERT: K 39 LEU cc_start: 0.9669 (pp) cc_final: 0.9356 (tp) REVERT: K 48 MET cc_start: 0.9308 (mmm) cc_final: 0.9062 (mmm) REVERT: K 97 ASN cc_start: 0.9370 (t0) cc_final: 0.8977 (p0) REVERT: L 87 TYR cc_start: 0.9324 (m-80) cc_final: 0.8836 (m-80) outliers start: 5 outliers final: 0 residues processed: 381 average time/residue: 0.3003 time to fit residues: 172.7587 Evaluate side-chains 283 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN G 64 GLN H 38 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 ASN ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 344 ASN I 440 ASN ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 614 GLN ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.6776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18841 Z= 0.245 Angle : 0.711 8.461 25570 Z= 0.384 Chirality : 0.046 0.230 2814 Planarity : 0.005 0.075 3281 Dihedral : 6.607 33.831 2530 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.40 % Favored : 92.47 % Rotamer: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % 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: -2.00 (0.17), residues: 2297 helix: -0.72 (0.24), residues: 399 sheet: -1.18 (0.21), residues: 590 loop : -1.59 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 560 HIS 0.004 0.001 HIS A 341 PHE 0.033 0.002 PHE I 349 TYR 0.020 0.002 TYR F 607 ARG 0.011 0.001 ARG L 39 *********************** 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 393 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 391 time to evaluate : 2.039 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 36 HIS cc_start: 0.7952 (m-70) cc_final: 0.7718 (m170) REVERT: A 65 MET cc_start: 0.9665 (ppp) cc_final: 0.9270 (ppp) REVERT: A 118 MET cc_start: 0.8168 (mmp) cc_final: 0.7663 (mmp) REVERT: A 121 MET cc_start: 0.8925 (mmp) cc_final: 0.8347 (tpp) REVERT: A 316 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8883 (mm-30) REVERT: A 348 GLU cc_start: 0.9608 (mm-30) cc_final: 0.9304 (mm-30) REVERT: A 377 LEU cc_start: 0.9385 (mt) cc_final: 0.9077 (tp) REVERT: A 395 MET cc_start: 0.9676 (ppp) cc_final: 0.9444 (ppp) REVERT: A 415 LEU cc_start: 0.9675 (mt) cc_final: 0.9386 (tp) REVERT: A 441 TRP cc_start: 0.9331 (m-10) cc_final: 0.9077 (m-90) REVERT: B 545 LEU cc_start: 0.9772 (mm) cc_final: 0.9395 (mm) REVERT: B 548 GLU cc_start: 0.9356 (tt0) cc_final: 0.8982 (mt-10) REVERT: B 549 ARG cc_start: 0.9586 (mtp180) cc_final: 0.9308 (mmm-85) REVERT: C 11 MET cc_start: 0.9578 (mmp) cc_final: 0.9202 (mmp) REVERT: C 27 TYR cc_start: 0.7537 (t80) cc_final: 0.7273 (t80) REVERT: C 35 ASN cc_start: 0.9557 (m-40) cc_final: 0.9292 (t0) REVERT: C 97 ASN cc_start: 0.9355 (t0) cc_final: 0.8995 (p0) REVERT: D 87 TYR cc_start: 0.9390 (m-80) cc_final: 0.8807 (m-80) REVERT: E 65 MET cc_start: 0.9077 (ppp) cc_final: 0.8759 (ppp) REVERT: E 87 LYS cc_start: 0.9680 (ptpt) cc_final: 0.9446 (ptpt) REVERT: E 156 ASN cc_start: 0.9208 (t0) cc_final: 0.8980 (p0) REVERT: E 316 GLU cc_start: 0.9231 (mm-30) cc_final: 0.9022 (mm-30) REVERT: E 395 MET cc_start: 0.9674 (ppp) cc_final: 0.9292 (ppp) REVERT: E 437 MET cc_start: 0.9190 (mmt) cc_final: 0.8882 (tpt) REVERT: F 549 ARG cc_start: 0.9208 (mmm160) cc_final: 0.8840 (tpm170) REVERT: F 553 ASP cc_start: 0.9284 (m-30) cc_final: 0.8483 (m-30) REVERT: F 554 GLN cc_start: 0.9232 (mm-40) cc_final: 0.8791 (mm110) REVERT: F 587 TRP cc_start: 0.8984 (m100) cc_final: 0.8453 (m100) REVERT: F 590 MET cc_start: 0.8058 (tpp) cc_final: 0.7852 (tpp) REVERT: F 607 TYR cc_start: 0.8997 (m-80) cc_final: 0.8770 (m-80) REVERT: G 11 MET cc_start: 0.9576 (mmp) cc_final: 0.9233 (mmp) REVERT: G 27 TYR cc_start: 0.7547 (t80) cc_final: 0.5156 (t80) REVERT: G 28 GLU cc_start: 0.9694 (mp0) cc_final: 0.9214 (pm20) REVERT: G 31 ASP cc_start: 0.9472 (m-30) cc_final: 0.9238 (t0) REVERT: G 69 MET cc_start: 0.9068 (pmm) cc_final: 0.8682 (pmm) REVERT: G 80 LEU cc_start: 0.9724 (tt) cc_final: 0.9520 (tt) REVERT: G 93 THR cc_start: 0.7789 (m) cc_final: 0.7424 (t) REVERT: G 101 GLU cc_start: 0.9675 (tp30) cc_final: 0.9385 (tt0) REVERT: H 36 TYR cc_start: 0.9316 (m-80) cc_final: 0.8992 (m-80) REVERT: H 38 GLN cc_start: 0.9627 (OUTLIER) cc_final: 0.9399 (pp30) REVERT: H 87 TYR cc_start: 0.9429 (m-80) cc_final: 0.8827 (m-80) REVERT: I 39 TRP cc_start: 0.7787 (m-90) cc_final: 0.7450 (m-90) REVERT: I 74 MET cc_start: 0.9787 (ppp) cc_final: 0.9474 (ppp) REVERT: I 121 MET cc_start: 0.9128 (mmp) cc_final: 0.8793 (tpp) REVERT: I 162 LEU cc_start: 0.8620 (tp) cc_final: 0.8266 (tp) REVERT: I 349 PHE cc_start: 0.9552 (m-10) cc_final: 0.9295 (m-10) REVERT: I 395 MET cc_start: 0.9659 (ppp) cc_final: 0.9194 (ppp) REVERT: I 400 ILE cc_start: 0.9329 (mt) cc_final: 0.9091 (pt) REVERT: I 437 MET cc_start: 0.8782 (tpp) cc_final: 0.8420 (tpt) REVERT: I 441 TRP cc_start: 0.8917 (m-10) cc_final: 0.8074 (m100) REVERT: I 454 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8814 (mm-30) REVERT: J 548 GLU cc_start: 0.9420 (tt0) cc_final: 0.9095 (mt-10) REVERT: K 11 MET cc_start: 0.9633 (mmp) cc_final: 0.9180 (mmp) REVERT: K 27 TYR cc_start: 0.7887 (t80) cc_final: 0.7363 (t80) REVERT: K 48 MET cc_start: 0.9320 (mmm) cc_final: 0.9110 (mmm) REVERT: K 69 MET cc_start: 0.8666 (pmm) cc_final: 0.8412 (pmm) REVERT: K 97 ASN cc_start: 0.9414 (t0) cc_final: 0.9049 (p0) REVERT: L 87 TYR cc_start: 0.9343 (m-80) cc_final: 0.8923 (m-80) outliers start: 2 outliers final: 0 residues processed: 393 average time/residue: 0.2903 time to fit residues: 172.1144 Evaluate side-chains 293 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 10.0000 chunk 200 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 103 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 overall best weight: 1.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 ASN F 617 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 ASN ** I 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18841 Z= 0.201 Angle : 0.681 9.878 25570 Z= 0.363 Chirality : 0.046 0.199 2814 Planarity : 0.005 0.078 3281 Dihedral : 6.246 33.695 2530 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.18 % Favored : 92.69 % Rotamer: Outliers : 0.15 % Allowed : 1.62 % Favored : 98.23 % 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: -1.84 (0.17), residues: 2297 helix: -0.48 (0.25), residues: 400 sheet: -1.06 (0.21), residues: 593 loop : -1.54 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 587 HIS 0.003 0.001 HIS A 218 PHE 0.033 0.002 PHE A 430 TYR 0.026 0.002 TYR J 550 ARG 0.006 0.001 ARG I 277 *********************** 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 390 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 387 time to evaluate : 2.084 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: A 9 TYR cc_start: 0.9315 (m-10) cc_final: 0.8855 (m-80) REVERT: A 65 MET cc_start: 0.9653 (ppp) cc_final: 0.9305 (ppp) REVERT: A 87 LYS cc_start: 0.9583 (ptpp) cc_final: 0.9324 (pttt) REVERT: A 118 MET cc_start: 0.8248 (mmp) cc_final: 0.7328 (tpp) REVERT: A 121 MET cc_start: 0.8874 (mmp) cc_final: 0.7697 (tpp) REVERT: A 239 ILE cc_start: 0.9485 (mm) cc_final: 0.8321 (mm) REVERT: A 251 LYS cc_start: 0.8490 (mptt) cc_final: 0.8211 (mmtm) REVERT: A 316 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8559 (mt-10) REVERT: A 344 ASN cc_start: 0.9305 (t0) cc_final: 0.9047 (t0) REVERT: A 377 LEU cc_start: 0.9332 (mt) cc_final: 0.9018 (tp) REVERT: A 395 MET cc_start: 0.9663 (ppp) cc_final: 0.9421 (ppp) REVERT: A 415 LEU cc_start: 0.9674 (mt) cc_final: 0.9416 (tp) REVERT: B 548 GLU cc_start: 0.9339 (tt0) cc_final: 0.9134 (tt0) REVERT: B 549 ARG cc_start: 0.9586 (mtp180) cc_final: 0.9233 (mmm-85) REVERT: C 11 MET cc_start: 0.9572 (mmp) cc_final: 0.9228 (mmp) REVERT: C 27 TYR cc_start: 0.7970 (t80) cc_final: 0.7061 (t80) REVERT: C 28 GLU cc_start: 0.9742 (mp0) cc_final: 0.9540 (mp0) REVERT: C 97 ASN cc_start: 0.9554 (t0) cc_final: 0.9184 (p0) REVERT: D 87 TYR cc_start: 0.9375 (m-80) cc_final: 0.8789 (m-80) REVERT: E 9 TYR cc_start: 0.9416 (m-10) cc_final: 0.8779 (m-80) REVERT: E 65 MET cc_start: 0.9066 (ppp) cc_final: 0.8728 (ppp) REVERT: E 121 MET cc_start: 0.9272 (mmm) cc_final: 0.8692 (mmm) REVERT: E 156 ASN cc_start: 0.9363 (t0) cc_final: 0.9089 (p0) REVERT: E 246 LEU cc_start: 0.9620 (mt) cc_final: 0.9305 (pt) REVERT: E 336 MET cc_start: 0.8642 (ppp) cc_final: 0.8404 (ppp) REVERT: E 395 MET cc_start: 0.9692 (ppp) cc_final: 0.9311 (ppp) REVERT: E 437 MET cc_start: 0.9250 (mmt) cc_final: 0.8965 (tpt) REVERT: F 538 LYS cc_start: 0.9373 (mmpt) cc_final: 0.9150 (mmtm) REVERT: F 587 TRP cc_start: 0.8983 (m100) cc_final: 0.8457 (m100) REVERT: F 607 TYR cc_start: 0.9046 (m-80) cc_final: 0.8793 (m-80) REVERT: G 11 MET cc_start: 0.9578 (mmp) cc_final: 0.9228 (mmp) REVERT: G 27 TYR cc_start: 0.7601 (t80) cc_final: 0.5320 (t80) REVERT: G 28 GLU cc_start: 0.9702 (mp0) cc_final: 0.9243 (pm20) REVERT: G 31 ASP cc_start: 0.9487 (m-30) cc_final: 0.9229 (t0) REVERT: G 69 MET cc_start: 0.9017 (pmm) cc_final: 0.8675 (pmm) REVERT: G 80 LEU cc_start: 0.9689 (tt) cc_final: 0.9403 (tt) REVERT: G 82 LEU cc_start: 0.9456 (tp) cc_final: 0.9059 (tp) REVERT: G 93 THR cc_start: 0.8044 (m) cc_final: 0.7698 (t) REVERT: G 101 GLU cc_start: 0.9686 (tp30) cc_final: 0.9393 (tt0) REVERT: H 36 TYR cc_start: 0.9306 (m-80) cc_final: 0.8966 (m-80) REVERT: I 39 TRP cc_start: 0.7703 (m-90) cc_final: 0.7370 (m-90) REVERT: I 74 MET cc_start: 0.9767 (ppp) cc_final: 0.9358 (ppp) REVERT: I 121 MET cc_start: 0.9094 (mmp) cc_final: 0.8711 (tpp) REVERT: I 164 ASN cc_start: 0.9035 (m-40) cc_final: 0.8738 (m-40) REVERT: I 239 ILE cc_start: 0.9295 (mm) cc_final: 0.8931 (mm) REVERT: I 312 GLU cc_start: 0.9717 (mt-10) cc_final: 0.9411 (mt-10) REVERT: I 316 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9115 (mm-30) REVERT: I 395 MET cc_start: 0.9665 (ppp) cc_final: 0.9186 (ppp) REVERT: I 400 ILE cc_start: 0.9313 (mt) cc_final: 0.9072 (pt) REVERT: I 415 LEU cc_start: 0.9645 (mt) cc_final: 0.9297 (tp) REVERT: I 437 MET cc_start: 0.8809 (tpp) cc_final: 0.8291 (tpt) REVERT: I 441 TRP cc_start: 0.8686 (m-10) cc_final: 0.7861 (m100) REVERT: I 454 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8216 (mp0) REVERT: J 548 GLU cc_start: 0.9412 (tt0) cc_final: 0.9058 (mt-10) REVERT: J 556 LEU cc_start: 0.9693 (tp) cc_final: 0.9453 (pp) REVERT: K 11 MET cc_start: 0.9605 (mmp) cc_final: 0.9077 (mmp) REVERT: K 18 MET cc_start: 0.9353 (tmm) cc_final: 0.9079 (tmm) REVERT: K 27 TYR cc_start: 0.7938 (t80) cc_final: 0.7430 (t80) REVERT: K 69 MET cc_start: 0.8633 (pmm) cc_final: 0.8379 (pmm) REVERT: K 97 ASN cc_start: 0.9284 (t0) cc_final: 0.8936 (p0) REVERT: L 87 TYR cc_start: 0.9332 (m-80) cc_final: 0.8911 (m-80) outliers start: 3 outliers final: 1 residues processed: 390 average time/residue: 0.2995 time to fit residues: 175.2594 Evaluate side-chains 294 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 293 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 125 optimal weight: 0.0980 chunk 187 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.7331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18841 Z= 0.188 Angle : 0.668 7.220 25570 Z= 0.358 Chirality : 0.045 0.178 2814 Planarity : 0.005 0.086 3281 Dihedral : 6.056 34.261 2530 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.92 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -1.80 (0.17), residues: 2297 helix: -0.49 (0.26), residues: 402 sheet: -1.03 (0.21), residues: 602 loop : -1.51 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 595 HIS 0.002 0.001 HIS K 102 PHE 0.026 0.002 PHE I 349 TYR 0.020 0.001 TYR J 550 ARG 0.008 0.001 ARG H 54 *********************** 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 387 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 2.119 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: A 10 TYR cc_start: 0.9109 (t80) cc_final: 0.7194 (p90) REVERT: A 65 MET cc_start: 0.9647 (ppp) cc_final: 0.9299 (ppp) REVERT: A 83 ASP cc_start: 0.9657 (t70) cc_final: 0.9457 (t0) REVERT: A 87 LYS cc_start: 0.9519 (ptpp) cc_final: 0.9308 (pttt) REVERT: A 118 MET cc_start: 0.8080 (mmp) cc_final: 0.7276 (tpp) REVERT: A 121 MET cc_start: 0.8811 (mmp) cc_final: 0.7742 (mmm) REVERT: A 239 ILE cc_start: 0.9446 (mm) cc_final: 0.8271 (mm) REVERT: A 251 LYS cc_start: 0.8646 (mptt) cc_final: 0.8360 (mmtm) REVERT: A 316 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8543 (mt-10) REVERT: A 377 LEU cc_start: 0.9289 (mt) cc_final: 0.9006 (tp) REVERT: A 395 MET cc_start: 0.9671 (ppp) cc_final: 0.9403 (ppp) REVERT: A 415 LEU cc_start: 0.9665 (mt) cc_final: 0.9405 (tp) REVERT: A 437 MET cc_start: 0.8782 (mmm) cc_final: 0.8567 (tpp) REVERT: B 544 VAL cc_start: 0.9794 (t) cc_final: 0.9584 (t) REVERT: B 545 LEU cc_start: 0.9790 (mm) cc_final: 0.9414 (mm) REVERT: B 548 GLU cc_start: 0.9394 (tt0) cc_final: 0.8971 (mt-10) REVERT: B 549 ARG cc_start: 0.9601 (mtp180) cc_final: 0.9337 (mtp180) REVERT: C 11 MET cc_start: 0.9554 (mmp) cc_final: 0.9171 (mmp) REVERT: C 28 GLU cc_start: 0.9661 (mp0) cc_final: 0.9445 (mp0) REVERT: C 97 ASN cc_start: 0.9505 (t0) cc_final: 0.9050 (p0) REVERT: D 87 TYR cc_start: 0.9378 (m-80) cc_final: 0.8739 (m-80) REVERT: E 9 TYR cc_start: 0.9381 (m-10) cc_final: 0.8738 (m-80) REVERT: E 16 LYS cc_start: 0.9627 (mmmt) cc_final: 0.9352 (mmtm) REVERT: E 65 MET cc_start: 0.9096 (ppp) cc_final: 0.8763 (ppp) REVERT: E 121 MET cc_start: 0.9294 (mmm) cc_final: 0.8665 (mmm) REVERT: E 156 ASN cc_start: 0.9370 (t0) cc_final: 0.9091 (p0) REVERT: E 246 LEU cc_start: 0.9602 (mt) cc_final: 0.9282 (pt) REVERT: E 336 MET cc_start: 0.8626 (ppp) cc_final: 0.8331 (ppp) REVERT: E 395 MET cc_start: 0.9703 (ppp) cc_final: 0.9316 (ppp) REVERT: E 437 MET cc_start: 0.9277 (mmt) cc_final: 0.8980 (tpt) REVERT: F 538 LYS cc_start: 0.9398 (mmpt) cc_final: 0.9147 (mmtm) REVERT: F 555 GLN cc_start: 0.9571 (tp40) cc_final: 0.9318 (pp30) REVERT: F 556 LEU cc_start: 0.9788 (tp) cc_final: 0.9580 (tp) REVERT: F 587 TRP cc_start: 0.8976 (m100) cc_final: 0.8424 (m100) REVERT: F 607 TYR cc_start: 0.9070 (m-80) cc_final: 0.8810 (m-80) REVERT: G 11 MET cc_start: 0.9581 (mmp) cc_final: 0.9192 (mmp) REVERT: G 27 TYR cc_start: 0.8152 (t80) cc_final: 0.5726 (t80) REVERT: G 28 GLU cc_start: 0.9706 (mp0) cc_final: 0.9146 (pm20) REVERT: G 31 ASP cc_start: 0.9463 (m-30) cc_final: 0.9231 (t0) REVERT: G 69 MET cc_start: 0.8978 (pmm) cc_final: 0.8759 (pmm) REVERT: G 93 THR cc_start: 0.7919 (m) cc_final: 0.7626 (t) REVERT: G 101 GLU cc_start: 0.9647 (tp30) cc_final: 0.9352 (tt0) REVERT: H 36 TYR cc_start: 0.9335 (m-80) cc_final: 0.8664 (m-80) REVERT: H 87 TYR cc_start: 0.9493 (m-10) cc_final: 0.8969 (m-80) REVERT: I 39 TRP cc_start: 0.7742 (m-90) cc_final: 0.7375 (m-90) REVERT: I 49 PRO cc_start: 0.7485 (Cg_exo) cc_final: 0.7252 (Cg_endo) REVERT: I 74 MET cc_start: 0.9763 (ppp) cc_final: 0.9387 (ppp) REVERT: I 121 MET cc_start: 0.9089 (mmp) cc_final: 0.8497 (tpp) REVERT: I 164 ASN cc_start: 0.9000 (m-40) cc_final: 0.8757 (m110) REVERT: I 239 ILE cc_start: 0.9282 (mm) cc_final: 0.8881 (mm) REVERT: I 316 GLU cc_start: 0.9276 (mm-30) cc_final: 0.9003 (mm-30) REVERT: I 395 MET cc_start: 0.9674 (ppp) cc_final: 0.9155 (ppp) REVERT: I 400 ILE cc_start: 0.9325 (mt) cc_final: 0.9103 (pt) REVERT: I 415 LEU cc_start: 0.9653 (mt) cc_final: 0.9315 (tp) REVERT: I 437 MET cc_start: 0.8704 (tpp) cc_final: 0.8279 (tpt) REVERT: I 441 TRP cc_start: 0.8508 (m-10) cc_final: 0.7694 (m100) REVERT: I 454 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8220 (mp0) REVERT: J 548 GLU cc_start: 0.9397 (tt0) cc_final: 0.8989 (mt-10) REVERT: J 551 LEU cc_start: 0.9827 (mt) cc_final: 0.9601 (pp) REVERT: J 556 LEU cc_start: 0.9685 (tp) cc_final: 0.9437 (pp) REVERT: K 11 MET cc_start: 0.9598 (mmp) cc_final: 0.9057 (mmp) REVERT: K 18 MET cc_start: 0.9396 (tmm) cc_final: 0.9126 (tmm) REVERT: K 23 ARG cc_start: 0.9552 (ttm110) cc_final: 0.9206 (mtm-85) REVERT: K 27 TYR cc_start: 0.8001 (t80) cc_final: 0.7472 (t80) REVERT: K 28 GLU cc_start: 0.9749 (mp0) cc_final: 0.9533 (mp0) REVERT: K 34 LEU cc_start: 0.9441 (mm) cc_final: 0.9105 (mm) REVERT: K 35 ASN cc_start: 0.9300 (m-40) cc_final: 0.8074 (p0) REVERT: K 51 LEU cc_start: 0.9343 (tp) cc_final: 0.9104 (tp) REVERT: K 69 MET cc_start: 0.8665 (pmm) cc_final: 0.8420 (pmm) REVERT: K 93 THR cc_start: 0.6671 (t) cc_final: 0.4989 (t) REVERT: K 97 ASN cc_start: 0.9285 (t0) cc_final: 0.8939 (p0) REVERT: K 100 ASP cc_start: 0.9649 (p0) cc_final: 0.9214 (p0) REVERT: L 87 TYR cc_start: 0.9341 (m-80) cc_final: 0.8912 (m-80) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.2872 time to fit residues: 168.0980 Evaluate side-chains 295 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.7633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18841 Z= 0.209 Angle : 0.675 7.911 25570 Z= 0.361 Chirality : 0.045 0.180 2814 Planarity : 0.005 0.086 3281 Dihedral : 6.038 33.962 2530 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.79 % Favored : 92.12 % Rotamer: Outliers : 0.05 % Allowed : 0.64 % 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: -1.71 (0.17), residues: 2297 helix: -0.47 (0.26), residues: 399 sheet: -1.00 (0.21), residues: 606 loop : -1.40 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 595 HIS 0.003 0.001 HIS I 185 PHE 0.020 0.002 PHE I 349 TYR 0.023 0.002 TYR J 550 ARG 0.010 0.001 ARG F 549 *********************** 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 375 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 374 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9000 (m-80) cc_final: 0.8499 (m-80) REVERT: A 65 MET cc_start: 0.9677 (ppp) cc_final: 0.9166 (ppp) REVERT: A 83 ASP cc_start: 0.9635 (t70) cc_final: 0.9381 (t0) REVERT: A 87 LYS cc_start: 0.9472 (ptpp) cc_final: 0.9189 (pttt) REVERT: A 118 MET cc_start: 0.7801 (mmp) cc_final: 0.7392 (mmt) REVERT: A 121 MET cc_start: 0.8841 (mmp) cc_final: 0.8360 (tpp) REVERT: A 239 ILE cc_start: 0.9463 (mm) cc_final: 0.8879 (mm) REVERT: A 251 LYS cc_start: 0.8860 (mptt) cc_final: 0.8526 (mmtm) REVERT: A 312 GLU cc_start: 0.9682 (mt-10) cc_final: 0.9308 (mt-10) REVERT: A 316 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8788 (mm-30) REVERT: A 344 ASN cc_start: 0.9093 (t0) cc_final: 0.8855 (t0) REVERT: A 395 MET cc_start: 0.9634 (ppp) cc_final: 0.9370 (ppp) REVERT: A 415 LEU cc_start: 0.9692 (mt) cc_final: 0.9419 (tp) REVERT: A 437 MET cc_start: 0.8699 (mmm) cc_final: 0.8475 (tmm) REVERT: A 440 ASN cc_start: 0.9679 (p0) cc_final: 0.9377 (p0) REVERT: A 441 TRP cc_start: 0.9194 (m-10) cc_final: 0.8756 (m100) REVERT: B 544 VAL cc_start: 0.9779 (t) cc_final: 0.9523 (t) REVERT: B 545 LEU cc_start: 0.9788 (mm) cc_final: 0.9405 (mm) REVERT: B 548 GLU cc_start: 0.9345 (tt0) cc_final: 0.8947 (mt-10) REVERT: B 549 ARG cc_start: 0.9609 (mtp180) cc_final: 0.9201 (mtp180) REVERT: C 11 MET cc_start: 0.9534 (mmp) cc_final: 0.9074 (mmp) REVERT: C 27 TYR cc_start: 0.7962 (t80) cc_final: 0.5376 (t80) REVERT: C 28 GLU cc_start: 0.9736 (mp0) cc_final: 0.9145 (pm20) REVERT: C 31 ASP cc_start: 0.9385 (m-30) cc_final: 0.9103 (t0) REVERT: C 51 LEU cc_start: 0.9457 (tp) cc_final: 0.9123 (tp) REVERT: C 97 ASN cc_start: 0.9463 (t0) cc_final: 0.9095 (p0) REVERT: D 36 TYR cc_start: 0.8099 (m-80) cc_final: 0.7143 (m-80) REVERT: D 87 TYR cc_start: 0.9332 (m-80) cc_final: 0.8622 (m-80) REVERT: E 9 TYR cc_start: 0.9410 (m-10) cc_final: 0.8832 (m-80) REVERT: E 10 TYR cc_start: 0.9655 (t80) cc_final: 0.8781 (t80) REVERT: E 16 LYS cc_start: 0.9633 (mmmt) cc_final: 0.9369 (mmtm) REVERT: E 65 MET cc_start: 0.9142 (ppp) cc_final: 0.8810 (ppp) REVERT: E 74 MET cc_start: 0.9571 (ppp) cc_final: 0.9330 (ppp) REVERT: E 87 LYS cc_start: 0.9593 (ptpp) cc_final: 0.9339 (pttt) REVERT: E 121 MET cc_start: 0.9294 (mmm) cc_final: 0.8709 (mmm) REVERT: E 156 ASN cc_start: 0.9410 (t0) cc_final: 0.9121 (p0) REVERT: E 246 LEU cc_start: 0.9640 (mt) cc_final: 0.9336 (pt) REVERT: E 336 MET cc_start: 0.8665 (ppp) cc_final: 0.8350 (ppp) REVERT: E 395 MET cc_start: 0.9725 (ppp) cc_final: 0.9331 (ppp) REVERT: E 437 MET cc_start: 0.9220 (mmt) cc_final: 0.8919 (tpt) REVERT: F 538 LYS cc_start: 0.9398 (mmpt) cc_final: 0.9146 (mmtm) REVERT: G 11 MET cc_start: 0.9588 (mmp) cc_final: 0.9317 (mmp) REVERT: G 27 TYR cc_start: 0.8130 (t80) cc_final: 0.5513 (t80) REVERT: G 28 GLU cc_start: 0.9699 (mp0) cc_final: 0.9073 (pm20) REVERT: G 31 ASP cc_start: 0.9442 (m-30) cc_final: 0.9074 (t0) REVERT: G 51 LEU cc_start: 0.9547 (tp) cc_final: 0.9337 (tp) REVERT: G 69 MET cc_start: 0.8992 (pmm) cc_final: 0.8756 (pmm) REVERT: G 93 THR cc_start: 0.7873 (m) cc_final: 0.7649 (t) REVERT: G 97 ASN cc_start: 0.9262 (t0) cc_final: 0.9060 (t0) REVERT: H 36 TYR cc_start: 0.9344 (m-80) cc_final: 0.8745 (m-80) REVERT: H 87 TYR cc_start: 0.9484 (m-10) cc_final: 0.9037 (m-80) REVERT: I 39 TRP cc_start: 0.7839 (m-90) cc_final: 0.7358 (m-90) REVERT: I 74 MET cc_start: 0.9750 (ppp) cc_final: 0.9392 (ppp) REVERT: I 76 GLU cc_start: 0.9512 (mp0) cc_final: 0.9310 (pm20) REVERT: I 77 ASP cc_start: 0.9712 (m-30) cc_final: 0.9474 (m-30) REVERT: I 121 MET cc_start: 0.9123 (mmp) cc_final: 0.8534 (tpp) REVERT: I 164 ASN cc_start: 0.8953 (m-40) cc_final: 0.8720 (m110) REVERT: I 239 ILE cc_start: 0.9245 (mm) cc_final: 0.8862 (mm) REVERT: I 316 GLU cc_start: 0.9323 (mm-30) cc_final: 0.9031 (mm-30) REVERT: I 343 PHE cc_start: 0.8753 (p90) cc_final: 0.8329 (p90) REVERT: I 395 MET cc_start: 0.9635 (ppp) cc_final: 0.9077 (ppp) REVERT: I 400 ILE cc_start: 0.9314 (mt) cc_final: 0.9085 (pt) REVERT: I 437 MET cc_start: 0.8759 (tpp) cc_final: 0.8316 (tpp) REVERT: I 441 TRP cc_start: 0.8624 (m-10) cc_final: 0.7631 (m100) REVERT: I 454 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8321 (mp0) REVERT: J 548 GLU cc_start: 0.9400 (tt0) cc_final: 0.8954 (tm-30) REVERT: J 551 LEU cc_start: 0.9833 (mt) cc_final: 0.9614 (pp) REVERT: J 556 LEU cc_start: 0.9694 (tp) cc_final: 0.9386 (pp) REVERT: K 18 MET cc_start: 0.9415 (tmm) cc_final: 0.9074 (tmm) REVERT: K 23 ARG cc_start: 0.9538 (ttm110) cc_final: 0.9198 (mtm-85) REVERT: K 27 TYR cc_start: 0.8030 (t80) cc_final: 0.7536 (t80) REVERT: K 28 GLU cc_start: 0.9751 (mp0) cc_final: 0.9536 (mp0) REVERT: K 51 LEU cc_start: 0.9368 (tp) cc_final: 0.9167 (tp) REVERT: K 93 THR cc_start: 0.6766 (t) cc_final: 0.6451 (t) REVERT: K 97 ASN cc_start: 0.9472 (t0) cc_final: 0.9155 (p0) REVERT: L 87 TYR cc_start: 0.9336 (m-80) cc_final: 0.8919 (m-80) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.2891 time to fit residues: 164.4179 Evaluate side-chains 290 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 195 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.8028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18841 Z= 0.249 Angle : 0.705 8.544 25570 Z= 0.378 Chirality : 0.045 0.194 2814 Planarity : 0.005 0.090 3281 Dihedral : 6.168 32.705 2530 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.79 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.73 (0.17), residues: 2297 helix: -0.63 (0.26), residues: 395 sheet: -0.88 (0.21), residues: 619 loop : -1.43 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 587 HIS 0.006 0.001 HIS K 102 PHE 0.025 0.002 PHE I 349 TYR 0.019 0.002 TYR G 100 ARG 0.006 0.001 ARG K 38 *********************** 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 365 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.345 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 65 MET cc_start: 0.9666 (ppp) cc_final: 0.9153 (ppp) REVERT: A 83 ASP cc_start: 0.9636 (t70) cc_final: 0.9379 (t0) REVERT: A 87 LYS cc_start: 0.9468 (ptpp) cc_final: 0.9188 (pttt) REVERT: A 118 MET cc_start: 0.7877 (mmp) cc_final: 0.7566 (mmt) REVERT: A 121 MET cc_start: 0.8878 (mmp) cc_final: 0.8424 (tpp) REVERT: A 239 ILE cc_start: 0.9422 (mm) cc_final: 0.8860 (mm) REVERT: A 251 LYS cc_start: 0.8936 (mptt) cc_final: 0.8579 (mmtm) REVERT: A 316 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8829 (mm-30) REVERT: A 388 TRP cc_start: 0.8809 (t-100) cc_final: 0.7908 (t-100) REVERT: A 395 MET cc_start: 0.9637 (ppp) cc_final: 0.9385 (ppp) REVERT: A 415 LEU cc_start: 0.9713 (mt) cc_final: 0.9434 (tp) REVERT: A 440 ASN cc_start: 0.9707 (p0) cc_final: 0.9398 (p0) REVERT: A 441 TRP cc_start: 0.9237 (m-10) cc_final: 0.8879 (m100) REVERT: B 544 VAL cc_start: 0.9779 (t) cc_final: 0.9513 (t) REVERT: B 545 LEU cc_start: 0.9789 (mm) cc_final: 0.9405 (mm) REVERT: B 548 GLU cc_start: 0.9350 (tt0) cc_final: 0.8920 (mt-10) REVERT: B 549 ARG cc_start: 0.9584 (mtp180) cc_final: 0.9192 (mtp180) REVERT: C 11 MET cc_start: 0.9522 (mmp) cc_final: 0.9072 (mmp) REVERT: C 28 GLU cc_start: 0.9724 (mp0) cc_final: 0.9522 (mp0) REVERT: C 51 LEU cc_start: 0.9450 (tp) cc_final: 0.9159 (tp) REVERT: C 86 ASP cc_start: 0.9132 (m-30) cc_final: 0.8896 (m-30) REVERT: C 97 ASN cc_start: 0.9474 (t0) cc_final: 0.9113 (p0) REVERT: D 36 TYR cc_start: 0.8012 (m-80) cc_final: 0.7150 (m-80) REVERT: D 87 TYR cc_start: 0.9336 (m-80) cc_final: 0.8692 (m-80) REVERT: E 10 TYR cc_start: 0.9536 (t80) cc_final: 0.9148 (t80) REVERT: E 15 TRP cc_start: 0.8147 (m-90) cc_final: 0.7924 (m-90) REVERT: E 16 LYS cc_start: 0.9615 (mmmt) cc_final: 0.9345 (mmtm) REVERT: E 49 PRO cc_start: 0.7442 (Cg_exo) cc_final: 0.7220 (Cg_endo) REVERT: E 65 MET cc_start: 0.9158 (ppp) cc_final: 0.8832 (ppp) REVERT: E 74 MET cc_start: 0.9606 (ppp) cc_final: 0.9265 (ppp) REVERT: E 87 LYS cc_start: 0.9583 (ptpp) cc_final: 0.9257 (pttt) REVERT: E 156 ASN cc_start: 0.9419 (t0) cc_final: 0.9188 (p0) REVERT: E 246 LEU cc_start: 0.9673 (mt) cc_final: 0.9344 (pt) REVERT: E 336 MET cc_start: 0.8725 (ppp) cc_final: 0.8443 (ppp) REVERT: E 388 TRP cc_start: 0.8553 (t-100) cc_final: 0.7902 (t-100) REVERT: E 395 MET cc_start: 0.9735 (ppp) cc_final: 0.9356 (ppp) REVERT: E 437 MET cc_start: 0.9220 (mmt) cc_final: 0.8673 (tpt) REVERT: E 440 ASN cc_start: 0.9475 (m110) cc_final: 0.9265 (m-40) REVERT: E 441 TRP cc_start: 0.9073 (m-10) cc_final: 0.8491 (m-90) REVERT: F 538 LYS cc_start: 0.9415 (mmpt) cc_final: 0.9169 (mmtm) REVERT: F 549 ARG cc_start: 0.9455 (tpm170) cc_final: 0.9176 (tpm170) REVERT: F 553 ASP cc_start: 0.9452 (t0) cc_final: 0.9190 (t0) REVERT: G 11 MET cc_start: 0.9593 (mmp) cc_final: 0.9248 (mmp) REVERT: G 27 TYR cc_start: 0.8148 (t80) cc_final: 0.5674 (t80) REVERT: G 28 GLU cc_start: 0.9672 (mp0) cc_final: 0.9033 (pm20) REVERT: G 31 ASP cc_start: 0.9454 (m-30) cc_final: 0.9116 (t0) REVERT: G 51 LEU cc_start: 0.9517 (tp) cc_final: 0.9300 (tp) REVERT: G 69 MET cc_start: 0.8993 (pmm) cc_final: 0.8738 (pmm) REVERT: G 93 THR cc_start: 0.8031 (m) cc_final: 0.7775 (t) REVERT: G 97 ASN cc_start: 0.9240 (t0) cc_final: 0.9027 (t0) REVERT: H 36 TYR cc_start: 0.9431 (m-80) cc_final: 0.8885 (m-80) REVERT: H 87 TYR cc_start: 0.9528 (m-10) cc_final: 0.9018 (m-80) REVERT: I 39 TRP cc_start: 0.7750 (m-90) cc_final: 0.7344 (m-90) REVERT: I 49 PRO cc_start: 0.7645 (Cg_exo) cc_final: 0.7425 (Cg_endo) REVERT: I 74 MET cc_start: 0.9768 (ppp) cc_final: 0.9396 (ppp) REVERT: I 121 MET cc_start: 0.9086 (mmp) cc_final: 0.8546 (tpp) REVERT: I 239 ILE cc_start: 0.9255 (mm) cc_final: 0.8942 (mm) REVERT: I 312 GLU cc_start: 0.9685 (mt-10) cc_final: 0.9257 (mm-30) REVERT: I 316 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9059 (mm-30) REVERT: I 343 PHE cc_start: 0.8730 (p90) cc_final: 0.8276 (p90) REVERT: I 388 TRP cc_start: 0.8235 (t-100) cc_final: 0.8014 (t-100) REVERT: I 395 MET cc_start: 0.9626 (ppp) cc_final: 0.8919 (ppp) REVERT: I 400 ILE cc_start: 0.9320 (mt) cc_final: 0.9084 (pt) REVERT: I 437 MET cc_start: 0.8706 (tpp) cc_final: 0.8149 (tpp) REVERT: I 441 TRP cc_start: 0.8636 (m-10) cc_final: 0.7707 (m100) REVERT: I 454 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8404 (mp0) REVERT: J 548 GLU cc_start: 0.9421 (tt0) cc_final: 0.8925 (tm-30) REVERT: J 551 LEU cc_start: 0.9853 (mt) cc_final: 0.9611 (pp) REVERT: K 11 MET cc_start: 0.9719 (mmp) cc_final: 0.9518 (mmp) REVERT: K 18 MET cc_start: 0.9425 (tmm) cc_final: 0.9082 (tmm) REVERT: K 23 ARG cc_start: 0.9569 (ttm110) cc_final: 0.9174 (mtm-85) REVERT: K 27 TYR cc_start: 0.7936 (t80) cc_final: 0.5467 (t80) REVERT: K 28 GLU cc_start: 0.9730 (mp0) cc_final: 0.9049 (pm20) REVERT: K 39 LEU cc_start: 0.9826 (pt) cc_final: 0.9445 (tp) REVERT: K 51 LEU cc_start: 0.9353 (tp) cc_final: 0.9150 (tp) REVERT: K 69 MET cc_start: 0.8982 (pmm) cc_final: 0.8571 (pmm) REVERT: K 97 ASN cc_start: 0.9519 (t0) cc_final: 0.9248 (p0) REVERT: L 36 TYR cc_start: 0.8707 (m-80) cc_final: 0.8028 (m-80) REVERT: L 87 TYR cc_start: 0.9346 (m-80) cc_final: 0.8856 (m-80) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.3014 time to fit residues: 168.2152 Evaluate side-chains 284 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 0.4980 chunk 218 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 298 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN ** B 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 589 ASN F 615 ASN ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.8473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 18841 Z= 0.332 Angle : 0.791 9.786 25570 Z= 0.425 Chirality : 0.047 0.271 2814 Planarity : 0.006 0.087 3281 Dihedral : 6.618 32.347 2530 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 31.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.27 % Favored : 89.60 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -1.89 (0.17), residues: 2297 helix: -0.92 (0.25), residues: 379 sheet: -1.04 (0.21), residues: 621 loop : -1.46 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 388 HIS 0.006 0.001 HIS A 341 PHE 0.031 0.003 PHE I 349 TYR 0.021 0.003 TYR E 140 ARG 0.008 0.001 ARG L 39 ********************** 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 339 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.030 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: A 9 TYR cc_start: 0.8954 (m-80) cc_final: 0.8706 (m-80) REVERT: A 39 TRP cc_start: 0.7968 (m-90) cc_final: 0.7732 (m-90) REVERT: A 65 MET cc_start: 0.9681 (ppp) cc_final: 0.9445 (ppp) REVERT: A 74 MET cc_start: 0.9643 (tmm) cc_final: 0.9439 (tmm) REVERT: A 83 ASP cc_start: 0.9658 (t70) cc_final: 0.9405 (t0) REVERT: A 87 LYS cc_start: 0.9446 (ptpp) cc_final: 0.9226 (pttt) REVERT: A 118 MET cc_start: 0.7777 (mmp) cc_final: 0.7487 (mmt) REVERT: A 121 MET cc_start: 0.8951 (mmp) cc_final: 0.8499 (tpp) REVERT: A 251 LYS cc_start: 0.9062 (mptt) cc_final: 0.8726 (mmtm) REVERT: A 312 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9462 (mt-10) REVERT: A 395 MET cc_start: 0.9638 (ppp) cc_final: 0.9364 (ppp) REVERT: A 415 LEU cc_start: 0.9728 (mt) cc_final: 0.9453 (tp) REVERT: A 437 MET cc_start: 0.8924 (tmm) cc_final: 0.8511 (tpt) REVERT: A 440 ASN cc_start: 0.9771 (p0) cc_final: 0.9417 (p0) REVERT: A 441 TRP cc_start: 0.8986 (m-10) cc_final: 0.8236 (m100) REVERT: B 548 GLU cc_start: 0.9397 (tt0) cc_final: 0.8925 (tm-30) REVERT: B 549 ARG cc_start: 0.9567 (mtp180) cc_final: 0.9168 (mtp180) REVERT: B 599 ILE cc_start: 0.9745 (mm) cc_final: 0.9533 (pt) REVERT: C 11 MET cc_start: 0.9479 (mmp) cc_final: 0.9213 (mmp) REVERT: C 27 TYR cc_start: 0.7810 (t80) cc_final: 0.5405 (t80) REVERT: C 28 GLU cc_start: 0.9711 (mp0) cc_final: 0.9125 (pm20) REVERT: C 31 ASP cc_start: 0.9445 (m-30) cc_final: 0.9195 (t0) REVERT: C 51 LEU cc_start: 0.9446 (tp) cc_final: 0.9147 (tp) REVERT: C 97 ASN cc_start: 0.9357 (t0) cc_final: 0.9060 (p0) REVERT: D 36 TYR cc_start: 0.8178 (m-80) cc_final: 0.7353 (m-80) REVERT: D 87 TYR cc_start: 0.9348 (m-80) cc_final: 0.8647 (m-80) REVERT: E 9 TYR cc_start: 0.9448 (m-10) cc_final: 0.8822 (m-80) REVERT: E 10 TYR cc_start: 0.9519 (t80) cc_final: 0.9057 (t80) REVERT: E 15 TRP cc_start: 0.8231 (m-90) cc_final: 0.7967 (m-90) REVERT: E 16 LYS cc_start: 0.9614 (mmmt) cc_final: 0.9335 (mmtm) REVERT: E 49 PRO cc_start: 0.7541 (Cg_exo) cc_final: 0.7335 (Cg_endo) REVERT: E 65 MET cc_start: 0.9251 (ppp) cc_final: 0.8976 (ppp) REVERT: E 74 MET cc_start: 0.9616 (ppp) cc_final: 0.9259 (ppp) REVERT: E 87 LYS cc_start: 0.9536 (ptpp) cc_final: 0.9256 (pttt) REVERT: E 156 ASN cc_start: 0.9452 (t0) cc_final: 0.9136 (p0) REVERT: E 246 LEU cc_start: 0.9708 (mt) cc_final: 0.9439 (pt) REVERT: E 336 MET cc_start: 0.8808 (ppp) cc_final: 0.8512 (ppp) REVERT: E 350 PHE cc_start: 0.9391 (m-10) cc_final: 0.8863 (m-80) REVERT: E 388 TRP cc_start: 0.8649 (t-100) cc_final: 0.8013 (t-100) REVERT: E 395 MET cc_start: 0.9749 (ppp) cc_final: 0.9356 (ppp) REVERT: E 437 MET cc_start: 0.9202 (mmt) cc_final: 0.8668 (tpp) REVERT: E 441 TRP cc_start: 0.9075 (m-10) cc_final: 0.8364 (m-90) REVERT: F 549 ARG cc_start: 0.9486 (tpm170) cc_final: 0.9137 (tpm170) REVERT: F 553 ASP cc_start: 0.9419 (t0) cc_final: 0.9165 (t0) REVERT: F 555 GLN cc_start: 0.9608 (tp40) cc_final: 0.9091 (tm-30) REVERT: F 556 LEU cc_start: 0.9818 (tp) cc_final: 0.9595 (tp) REVERT: F 559 ILE cc_start: 0.9300 (mt) cc_final: 0.8859 (mt) REVERT: G 11 MET cc_start: 0.9582 (mmp) cc_final: 0.9199 (mmp) REVERT: G 27 TYR cc_start: 0.8203 (t80) cc_final: 0.5707 (t80) REVERT: G 28 GLU cc_start: 0.9653 (mp0) cc_final: 0.9091 (pm20) REVERT: G 31 ASP cc_start: 0.9482 (m-30) cc_final: 0.9107 (t0) REVERT: G 69 MET cc_start: 0.9034 (pmm) cc_final: 0.8653 (pmm) REVERT: G 86 ASP cc_start: 0.9155 (m-30) cc_final: 0.8947 (m-30) REVERT: G 97 ASN cc_start: 0.9193 (t0) cc_final: 0.8976 (t0) REVERT: H 36 TYR cc_start: 0.9487 (m-80) cc_final: 0.9092 (m-80) REVERT: H 87 TYR cc_start: 0.9517 (m-10) cc_final: 0.9088 (m-80) REVERT: I 9 TYR cc_start: 0.9362 (m-80) cc_final: 0.9038 (m-80) REVERT: I 39 TRP cc_start: 0.7701 (m-90) cc_final: 0.7262 (m-90) REVERT: I 49 PRO cc_start: 0.7769 (Cg_exo) cc_final: 0.7556 (Cg_endo) REVERT: I 121 MET cc_start: 0.9213 (mmp) cc_final: 0.8285 (tpp) REVERT: I 239 ILE cc_start: 0.9181 (mm) cc_final: 0.8821 (mm) REVERT: I 312 GLU cc_start: 0.9677 (mt-10) cc_final: 0.9391 (mt-10) REVERT: I 316 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9106 (mm-30) REVERT: I 343 PHE cc_start: 0.8696 (p90) cc_final: 0.8162 (p90) REVERT: I 387 MET cc_start: 0.7960 (tmm) cc_final: 0.7647 (tmm) REVERT: I 388 TRP cc_start: 0.8278 (t-100) cc_final: 0.7957 (t-100) REVERT: I 395 MET cc_start: 0.9597 (ppp) cc_final: 0.9065 (ppp) REVERT: I 400 ILE cc_start: 0.9343 (mt) cc_final: 0.9117 (pt) REVERT: I 454 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8403 (mp0) REVERT: J 548 GLU cc_start: 0.9422 (tt0) cc_final: 0.9049 (tm-30) REVERT: J 549 ARG cc_start: 0.9558 (mtt-85) cc_final: 0.9327 (mtp85) REVERT: J 556 LEU cc_start: 0.9714 (tp) cc_final: 0.9425 (pp) REVERT: J 607 TYR cc_start: 0.8827 (m-80) cc_final: 0.8535 (m-80) REVERT: K 18 MET cc_start: 0.9436 (tmm) cc_final: 0.9162 (tmm) REVERT: K 23 ARG cc_start: 0.9565 (ttm110) cc_final: 0.9183 (mtm-85) REVERT: K 27 TYR cc_start: 0.7886 (t80) cc_final: 0.5815 (t80) REVERT: K 28 GLU cc_start: 0.9699 (mp0) cc_final: 0.9038 (pm20) REVERT: K 39 LEU cc_start: 0.9865 (pt) cc_final: 0.9021 (tp) REVERT: K 69 MET cc_start: 0.8989 (pmm) cc_final: 0.8625 (pmm) REVERT: K 97 ASN cc_start: 0.9266 (t0) cc_final: 0.8935 (p0) REVERT: K 100 ASP cc_start: 0.9461 (p0) cc_final: 0.9237 (p0) REVERT: L 36 TYR cc_start: 0.8727 (m-80) cc_final: 0.8276 (m-80) REVERT: L 87 TYR cc_start: 0.9331 (m-80) cc_final: 0.8839 (m-80) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2769 time to fit residues: 143.7484 Evaluate side-chains 273 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN A 164 ASN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 604 GLN ** F 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.039240 restraints weight = 161451.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.040684 restraints weight = 101846.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.041778 restraints weight = 71744.569| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.9105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 18841 Z= 0.405 Angle : 0.882 9.913 25570 Z= 0.477 Chirality : 0.049 0.226 2814 Planarity : 0.006 0.084 3281 Dihedral : 7.230 36.722 2530 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 37.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.10 % Favored : 88.72 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (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: -2.29 (0.17), residues: 2297 helix: -1.59 (0.23), residues: 374 sheet: -1.14 (0.21), residues: 620 loop : -1.69 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 560 HIS 0.007 0.002 HIS I 341 PHE 0.030 0.004 PHE D 62 TYR 0.027 0.003 TYR I 186 ARG 0.012 0.001 ARG L 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4093.72 seconds wall clock time: 75 minutes 6.73 seconds (4506.73 seconds total)