Starting phenix.real_space_refine on Sat Mar 16 07:26:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqs_23951/03_2024/7mqs_23951.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqs_23951/03_2024/7mqs_23951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqs_23951/03_2024/7mqs_23951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqs_23951/03_2024/7mqs_23951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqs_23951/03_2024/7mqs_23951.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqs_23951/03_2024/7mqs_23951.pdb" } resolution = 4.4 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= 0.048 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 114 5.16 5 C 8894 2.51 5 N 2403 2.21 5 O 2617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 575": "OE1" <-> "OE2" Residue "E GLU 695": "OE1" <-> "OE2" Residue "E TYR 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 533": "OD1" <-> "OD2" Residue "F TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 14028 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 6521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6521 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 762} Chain breaks: 6 Chain: "F" Number of atoms: 6563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6563 Classifications: {'peptide': 811} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 767} Chain breaks: 5 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 121 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "G" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "H" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Time building chain proxies: 6.62, per 1000 atoms: 0.47 Number of scatterers: 14028 At special positions: 0 Unit cell: (158.34, 101.01, 173.355, 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 114 16.00 O 2617 8.00 N 2403 7.00 C 8894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.03 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.02 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.04 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.04 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 647 " - pdb=" SG CYS E 860 " distance=2.03 Simple disulfide: pdb=" SG CYS E 786 " - pdb=" SG CYS E 795 " distance=2.03 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.03 Simple disulfide: pdb=" SG CYS F 192 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.04 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.02 Simple disulfide: pdb=" SG CYS F 647 " - pdb=" SG CYS F 860 " distance=2.04 Simple disulfide: pdb=" SG CYS F 786 " - pdb=" SG CYS F 795 " distance=2.03 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.02 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.02 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=2.05 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 19 " distance=2.04 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 11 " distance=2.03 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS H 7 " distance=2.02 Simple disulfide: pdb=" SG CYS G 20 " - pdb=" SG CYS H 19 " distance=2.04 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: 4.80 Conformation dependent library (CDL) restraints added in 2.4 seconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3288 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 33 sheets defined 13.5% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 255 through 266 Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 351 through 359 Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 496 through 500 removed outlier: 3.823A pdb=" N LEU E 500 " --> pdb=" O PHE E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 714 removed outlier: 3.670A pdb=" N GLU E 697 " --> pdb=" O LEU E 693 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER E 699 " --> pdb=" O GLU E 695 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER E 700 " --> pdb=" O LEU E 696 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG E 702 " --> pdb=" O GLU E 698 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 703 " --> pdb=" O SER E 699 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR E 708 " --> pdb=" O THR E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 870 Processing helix chain 'F' and resid 16 through 24 removed outlier: 4.363A pdb=" N ARG F 19 " --> pdb=" O ASN F 16 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 20 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS F 21 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU F 22 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 23 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU F 24 " --> pdb=" O HIS F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 16 through 24' Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.798A pdb=" N PHE F 46 " --> pdb=" O PRO F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 255 through 265 removed outlier: 3.676A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 262 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS F 263 " --> pdb=" O CYS F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 350 through 358 removed outlier: 3.871A pdb=" N GLU F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 444 removed outlier: 3.739A pdb=" N ILE F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 697 through 707 removed outlier: 3.571A pdb=" N PHE F 701 " --> pdb=" O GLU F 697 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG F 702 " --> pdb=" O GLU F 698 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS F 703 " --> pdb=" O SER F 699 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 704 " --> pdb=" O SER F 700 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE F 705 " --> pdb=" O PHE F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 813 removed outlier: 3.874A pdb=" N ASP F 812 " --> pdb=" O ALA F 809 " (cutoff:3.500A) Processing helix chain 'F' and resid 862 through 870 removed outlier: 3.678A pdb=" N GLU F 869 " --> pdb=" O HIS F 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.947A pdb=" N LEU C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 23 " --> pdb=" O TYR C 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 18 Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 13 through 19 Processing helix chain 'H' and resid 9 through 19 removed outlier: 3.654A pdb=" N CYS H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 7 through 13 removed outlier: 5.595A pdb=" N HIS E 32 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP E 12 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN E 34 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 29 " --> pdb=" O MET E 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 7 through 13 removed outlier: 5.595A pdb=" N HIS E 32 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP E 12 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN E 34 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LEU E 62 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU E 33 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N PHE E 64 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE E 35 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU E 61 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N PHE E 96 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU E 63 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU E 93 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLU E 120 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE E 95 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 212 through 216 removed outlier: 3.819A pdb=" N ALA E 227 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ASN E 215 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N CYS E 225 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 232 Processing sheet with id=AA5, first strand: chain 'E' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'E' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'E' and resid 292 through 295 removed outlier: 3.519A pdb=" N ASN E 295 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU E 300 " --> pdb=" O ASN E 295 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 311 through 321 removed outlier: 10.321A pdb=" N VAL E 335 " --> pdb=" O HIS E 313 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N LEU E 315 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 9.836A pdb=" N ASN E 337 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY E 317 " --> pdb=" O ASN E 337 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE E 341 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N LYS E 369 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU E 340 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG E 371 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE E 342 " --> pdb=" O ARG E 371 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE E 427 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR E 401 " --> pdb=" O PHE E 427 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N HIS E 429 " --> pdb=" O TYR E 401 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU E 403 " --> pdb=" O HIS E 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 363 through 364 removed outlier: 4.012A pdb=" N ILE E 364 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 475 through 479 removed outlier: 3.744A pdb=" N ILE E 485 " --> pdb=" O MET E 553 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 532 through 534 removed outlier: 3.562A pdb=" N VAL E 532 " --> pdb=" O LEU E 505 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 505 " --> pdb=" O VAL E 532 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE E 503 " --> pdb=" O ILE E 534 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY E 502 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE E 565 " --> pdb=" O PHE E 506 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 588 " --> pdb=" O TYR E 562 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 564 " --> pdb=" O ILE E 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 611 through 614 Processing sheet with id=AB4, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.606A pdb=" N GLU E 760 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN E 788 " --> pdb=" O ARG E 794 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 759 through 762 removed outlier: 3.606A pdb=" N GLU E 760 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 801 " --> pdb=" O ILE E 781 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 818 through 822 removed outlier: 3.524A pdb=" N HIS E 829 " --> pdb=" O GLU E 821 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 856 through 861 Processing sheet with id=AB8, first strand: chain 'E' and resid 856 through 861 removed outlier: 3.688A pdb=" N VAL E 884 " --> pdb=" O THR E 901 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 901 " --> pdb=" O VAL E 884 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 12 through 15 removed outlier: 4.439A pdb=" N ASN F 15 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET F 38 " --> pdb=" O ASN F 15 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL F 66 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU F 61 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE F 96 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU F 63 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU F 93 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLU F 120 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE F 95 " --> pdb=" O GLU F 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 28 through 29 removed outlier: 3.916A pdb=" N ILE F 57 " --> pdb=" O VAL F 81 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 171 through 173 removed outlier: 3.741A pdb=" N VAL F 179 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 212 through 216 removed outlier: 3.952A pdb=" N ALA F 227 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASN F 215 " --> pdb=" O CYS F 225 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N CYS F 225 " --> pdb=" O ASN F 215 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 231 through 233 Processing sheet with id=AC5, first strand: chain 'F' and resid 246 through 248 Processing sheet with id=AC6, first strand: chain 'F' and resid 278 through 279 Processing sheet with id=AC7, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AC8, first strand: chain 'F' and resid 311 through 321 removed outlier: 3.979A pdb=" N LEU F 314 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER F 339 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLU F 316 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N ILE F 341 " --> pdb=" O GLU F 316 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N GLU F 318 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N LEU F 403 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE F 370 " --> pdb=" O LEU F 403 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 311 through 321 removed outlier: 3.979A pdb=" N LEU F 314 " --> pdb=" O ASN F 337 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N SER F 339 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLU F 316 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 10.017A pdb=" N ILE F 341 " --> pdb=" O GLU F 316 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N GLU F 318 " --> pdb=" O ILE F 341 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 475 through 480 removed outlier: 3.881A pdb=" N ILE F 485 " --> pdb=" O MET F 553 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET F 553 " --> pdb=" O ILE F 485 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 530 through 534 removed outlier: 3.567A pdb=" N THR F 530 " --> pdb=" O TYR F 507 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR F 507 " --> pdb=" O THR F 530 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL F 532 " --> pdb=" O LEU F 505 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 505 " --> pdb=" O VAL F 532 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 567 " --> pdb=" O MET F 504 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 602 through 604 Processing sheet with id=AD4, first strand: chain 'F' and resid 759 through 762 removed outlier: 3.580A pdb=" N ALA F 799 " --> pdb=" O LEU F 783 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 819 through 822 Processing sheet with id=AD6, first strand: chain 'F' and resid 857 through 861 removed outlier: 4.229A pdb=" N LEU F 857 " --> pdb=" O TYR F 849 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR F 849 " --> pdb=" O LEU F 857 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU F 859 " --> pdb=" O VAL F 847 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 846 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: 5.04 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3196 1.33 - 1.46: 4217 1.46 - 1.59: 6804 1.59 - 1.72: 3 1.72 - 1.85: 136 Bond restraints: 14356 Sorted by residual: bond pdb=" C THR F 302 " pdb=" N PRO F 303 " ideal model delta sigma weight residual 1.332 1.403 -0.072 1.32e-02 5.74e+03 2.95e+01 bond pdb=" C THR E 790 " pdb=" N PRO E 791 " ideal model delta sigma weight residual 1.334 1.457 -0.124 2.34e-02 1.83e+03 2.79e+01 bond pdb=" C THR F 790 " pdb=" N PRO F 791 " ideal model delta sigma weight residual 1.334 1.434 -0.100 2.34e-02 1.83e+03 1.84e+01 bond pdb=" CB ASN F 349 " pdb=" CG ASN F 349 " ideal model delta sigma weight residual 1.516 1.613 -0.097 2.50e-02 1.60e+03 1.50e+01 bond pdb=" C LEU G 16 " pdb=" N GLU G 17 " ideal model delta sigma weight residual 1.333 1.386 -0.053 1.49e-02 4.50e+03 1.25e+01 ... (remaining 14351 not shown) Histogram of bond angle deviations from ideal: 93.19 - 103.42: 125 103.42 - 113.64: 7635 113.64 - 123.87: 10956 123.87 - 134.09: 723 134.09 - 144.32: 18 Bond angle restraints: 19457 Sorted by residual: angle pdb=" CA LEU E 37 " pdb=" CB LEU E 37 " pdb=" CG LEU E 37 " ideal model delta sigma weight residual 116.30 142.28 -25.98 3.50e+00 8.16e-02 5.51e+01 angle pdb=" C GLU F 469 " pdb=" N ASN F 470 " pdb=" CA ASN F 470 " ideal model delta sigma weight residual 121.54 135.41 -13.87 1.91e+00 2.74e-01 5.27e+01 angle pdb=" C PRO F 791 " pdb=" N GLU F 792 " pdb=" CA GLU F 792 " ideal model delta sigma weight residual 121.54 135.36 -13.82 1.91e+00 2.74e-01 5.24e+01 angle pdb=" CA ARG E 870 " pdb=" CB ARG E 870 " pdb=" CG ARG E 870 " ideal model delta sigma weight residual 114.10 128.39 -14.29 2.00e+00 2.50e-01 5.10e+01 angle pdb=" C THR F 578 " pdb=" N TYR F 579 " pdb=" CA TYR F 579 " ideal model delta sigma weight residual 121.54 135.15 -13.61 1.91e+00 2.74e-01 5.07e+01 ... (remaining 19452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 7570 17.32 - 34.64: 964 34.64 - 51.97: 160 51.97 - 69.29: 36 69.29 - 86.61: 12 Dihedral angle restraints: 8742 sinusoidal: 3654 harmonic: 5088 Sorted by residual: dihedral pdb=" CA THR F 578 " pdb=" C THR F 578 " pdb=" N TYR F 579 " pdb=" CA TYR F 579 " ideal model delta harmonic sigma weight residual 180.00 120.81 59.19 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CB CYS G 6 " pdb=" SG CYS G 6 " pdb=" SG CYS G 11 " pdb=" CB CYS G 11 " ideal model delta sinusoidal sigma weight residual 93.00 175.99 -82.99 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CA ASN E 111 " pdb=" C ASN E 111 " pdb=" N ILE E 112 " pdb=" CA ILE E 112 " ideal model delta harmonic sigma weight residual 180.00 137.85 42.15 0 5.00e+00 4.00e-02 7.11e+01 ... (remaining 8739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 2018 0.181 - 0.362: 81 0.362 - 0.543: 20 0.543 - 0.725: 8 0.725 - 0.906: 1 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CB ILE F 342 " pdb=" CA ILE F 342 " pdb=" CG1 ILE F 342 " pdb=" CG2 ILE F 342 " both_signs ideal model delta sigma weight residual False 2.64 1.74 0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CB ILE F 57 " pdb=" CA ILE F 57 " pdb=" CG1 ILE F 57 " pdb=" CG2 ILE F 57 " both_signs ideal model delta sigma weight residual False 2.64 1.95 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CB VAL E 712 " pdb=" CA VAL E 712 " pdb=" CG1 VAL E 712 " pdb=" CG2 VAL E 712 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.21e+01 ... (remaining 2125 not shown) Planarity restraints: 2511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 2 " 0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ILE A 2 " -0.078 2.00e-02 2.50e+03 pdb=" O ILE A 2 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL A 3 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 94 " -0.021 2.00e-02 2.50e+03 4.27e-02 1.83e+01 pdb=" C VAL F 94 " 0.074 2.00e-02 2.50e+03 pdb=" O VAL F 94 " -0.028 2.00e-02 2.50e+03 pdb=" N ILE F 95 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 708 " -0.004 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR F 708 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR F 708 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR F 708 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR F 708 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR F 708 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 708 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR F 708 " 0.001 2.00e-02 2.50e+03 ... (remaining 2508 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 5125 2.91 - 3.41: 10746 3.41 - 3.91: 25001 3.91 - 4.40: 24779 4.40 - 4.90: 42077 Nonbonded interactions: 107728 Sorted by model distance: nonbonded pdb=" O MET E 442 " pdb=" OG SER E 446 " model vdw 2.416 2.440 nonbonded pdb=" O VAL E 715 " pdb=" OG SER G 22 " model vdw 2.418 2.440 nonbonded pdb=" OE2 GLU E 698 " pdb=" OH TYR F 144 " model vdw 2.418 2.440 nonbonded pdb=" OG SER E 573 " pdb=" OE1 GLU E 575 " model vdw 2.419 2.440 nonbonded pdb=" OG SER F 481 " pdb=" O LYS F 484 " model vdw 2.420 2.440 ... (remaining 107723 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' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = (chain 'H' and resid 5 through 20) } ncs_group { reference = (chain 'E' and (resid 5 through 656 or resid 696 through 710 or resid 754 throug \ h 910)) selection = (chain 'F' and (resid 5 through 172 or resid 177 through 267 or resid 274 throug \ h 515 or resid 531 through 910)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 4.210 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 37.190 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.015 0.124 14356 Z= 0.982 Angle : 1.726 25.984 19457 Z= 0.883 Chirality : 0.102 0.906 2128 Planarity : 0.011 0.098 2511 Dihedral : 15.001 86.609 5322 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.59 % Allowed : 9.64 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -3.94 (0.17), residues: 1701 helix: -4.98 (0.10), residues: 236 sheet: -0.80 (0.30), residues: 282 loop : -2.77 (0.15), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP F 897 HIS 0.013 0.002 HIS F 263 PHE 0.053 0.005 PHE E 497 TYR 0.059 0.004 TYR F 708 ARG 0.012 0.001 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 110 MET cc_start: 0.7856 (mpp) cc_final: 0.5668 (tpp) REVERT: E 382 PHE cc_start: 0.9112 (m-80) cc_final: 0.8269 (m-80) REVERT: E 849 TYR cc_start: 0.9183 (p90) cc_final: 0.8867 (p90) REVERT: E 859 LEU cc_start: 0.9189 (tp) cc_final: 0.8760 (pp) REVERT: F 38 MET cc_start: 0.7623 (mmp) cc_final: 0.7197 (mmp) REVERT: F 90 ASN cc_start: 0.7816 (p0) cc_final: 0.7579 (p0) REVERT: F 292 TYR cc_start: 0.8507 (m-80) cc_final: 0.8197 (m-80) REVERT: F 830 LEU cc_start: 0.8427 (tp) cc_final: 0.8095 (mm) REVERT: F 831 MET cc_start: 0.7627 (mpp) cc_final: 0.6950 (mpp) REVERT: D 15 LEU cc_start: 0.8957 (mm) cc_final: 0.8747 (mm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2503 time to fit residues: 49.5240 Evaluate side-chains 85 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 50.0000 chunk 154 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 21 HIS ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 HIS E 230 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 610 GLN E 627 HIS ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 GLN ** F 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14356 Z= 0.361 Angle : 0.843 13.902 19457 Z= 0.428 Chirality : 0.048 0.205 2128 Planarity : 0.006 0.059 2511 Dihedral : 7.304 42.612 1899 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.94 % Favored : 92.65 % Rotamer: Outliers : 0.06 % Allowed : 6.87 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.97 (0.18), residues: 1701 helix: -3.32 (0.24), residues: 218 sheet: -0.47 (0.29), residues: 325 loop : -2.30 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 251 HIS 0.009 0.002 HIS E 417 PHE 0.024 0.002 PHE F 64 TYR 0.020 0.002 TYR F 492 ARG 0.008 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 MET cc_start: 0.4725 (ppp) cc_final: 0.4404 (ppp) REVERT: E 83 ARG cc_start: 0.7864 (ttt90) cc_final: 0.7380 (tpp-160) REVERT: E 428 PHE cc_start: 0.9032 (m-10) cc_final: 0.8732 (m-10) REVERT: E 844 LEU cc_start: 0.9602 (mm) cc_final: 0.9266 (mm) REVERT: E 859 LEU cc_start: 0.9046 (tp) cc_final: 0.8806 (tt) REVERT: F 831 MET cc_start: 0.7027 (mpp) cc_final: 0.6662 (mpp) REVERT: G 4 GLU cc_start: 0.7941 (pm20) cc_final: 0.7601 (pm20) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.2391 time to fit residues: 34.5757 Evaluate side-chains 66 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 chunk 128 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 ASN E 90 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 HIS ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14356 Z= 0.227 Angle : 0.690 12.201 19457 Z= 0.351 Chirality : 0.046 0.191 2128 Planarity : 0.004 0.050 2511 Dihedral : 6.568 45.897 1899 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.23 % Favored : 92.36 % Rotamer: Outliers : 0.19 % Allowed : 5.10 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.51 (0.19), residues: 1701 helix: -2.20 (0.31), residues: 221 sheet: -0.17 (0.31), residues: 296 loop : -2.11 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 414 HIS 0.006 0.001 HIS E 199 PHE 0.021 0.002 PHE F 64 TYR 0.015 0.002 TYR F 512 ARG 0.007 0.001 ARG F 873 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 MET cc_start: 0.5455 (ppp) cc_final: 0.5181 (ppp) REVERT: E 83 ARG cc_start: 0.7503 (ttt90) cc_final: 0.6541 (tpt170) REVERT: E 330 LEU cc_start: 0.7680 (tp) cc_final: 0.7479 (tp) REVERT: E 428 PHE cc_start: 0.9081 (m-10) cc_final: 0.8776 (m-10) REVERT: E 844 LEU cc_start: 0.9135 (mm) cc_final: 0.8588 (mm) REVERT: E 859 LEU cc_start: 0.9041 (tp) cc_final: 0.8796 (tt) REVERT: F 98 MET cc_start: 0.8515 (tpp) cc_final: 0.8173 (tpp) REVERT: F 404 ASP cc_start: 0.8378 (m-30) cc_final: 0.7948 (t0) REVERT: F 642 PHE cc_start: 0.7317 (m-80) cc_final: 0.7059 (m-80) REVERT: G 4 GLU cc_start: 0.8103 (pm20) cc_final: 0.7731 (pm20) outliers start: 3 outliers final: 2 residues processed: 96 average time/residue: 0.2378 time to fit residues: 35.5044 Evaluate side-chains 76 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.1980 chunk 73 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 164 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 405 ASN E 407 ASN F 90 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 429 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14356 Z= 0.186 Angle : 0.648 11.703 19457 Z= 0.328 Chirality : 0.046 0.208 2128 Planarity : 0.004 0.040 2511 Dihedral : 6.201 44.481 1899 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.17 % Favored : 92.36 % Rotamer: Outliers : 0.06 % Allowed : 3.84 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.30 (0.19), residues: 1701 helix: -1.89 (0.32), residues: 225 sheet: -0.14 (0.31), residues: 298 loop : -1.96 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 414 HIS 0.009 0.001 HIS E 199 PHE 0.026 0.001 PHE E 88 TYR 0.017 0.001 TYR F 3 ARG 0.003 0.000 ARG F 794 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 428 PHE cc_start: 0.9098 (m-10) cc_final: 0.8776 (m-10) REVERT: E 859 LEU cc_start: 0.9009 (tp) cc_final: 0.8726 (tt) REVERT: F 404 ASP cc_start: 0.8239 (m-30) cc_final: 0.7813 (t70) REVERT: D 15 LEU cc_start: 0.8990 (mm) cc_final: 0.8785 (mm) REVERT: G 4 GLU cc_start: 0.7927 (pm20) cc_final: 0.7573 (pm20) outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.2389 time to fit residues: 35.5417 Evaluate side-chains 73 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 140 optimal weight: 0.0000 chunk 113 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 407 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS F 276 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14356 Z= 0.271 Angle : 0.704 11.375 19457 Z= 0.356 Chirality : 0.046 0.247 2128 Planarity : 0.004 0.037 2511 Dihedral : 6.195 46.275 1899 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.11 % Favored : 90.53 % Rotamer: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.15 (0.20), residues: 1701 helix: -1.63 (0.32), residues: 241 sheet: -0.19 (0.30), residues: 311 loop : -1.85 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 414 HIS 0.008 0.001 HIS E 199 PHE 0.024 0.002 PHE E 88 TYR 0.032 0.002 TYR F 708 ARG 0.011 0.001 ARG E 887 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 LEU cc_start: 0.8926 (tp) cc_final: 0.8719 (pt) REVERT: E 386 ARG cc_start: 0.6457 (mmt180) cc_final: 0.5990 (tpt170) REVERT: E 428 PHE cc_start: 0.9184 (m-10) cc_final: 0.8878 (m-10) REVERT: E 845 TYR cc_start: 0.8832 (m-80) cc_final: 0.8515 (m-80) REVERT: E 847 VAL cc_start: 0.9534 (t) cc_final: 0.9237 (t) REVERT: E 859 LEU cc_start: 0.9078 (tp) cc_final: 0.8680 (tt) REVERT: F 294 MET cc_start: 0.8183 (pmm) cc_final: 0.7921 (mmm) REVERT: F 404 ASP cc_start: 0.8398 (m-30) cc_final: 0.7931 (t70) REVERT: F 642 PHE cc_start: 0.7325 (m-80) cc_final: 0.7056 (m-80) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.2291 time to fit residues: 36.0789 Evaluate side-chains 74 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 96 optimal weight: 0.0070 chunk 40 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 GLN E 407 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 635 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 HIS F 249 GLN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14356 Z= 0.346 Angle : 0.790 11.218 19457 Z= 0.400 Chirality : 0.048 0.186 2128 Planarity : 0.005 0.059 2511 Dihedral : 6.555 47.856 1899 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 25.51 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.64 % Favored : 88.95 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.19 (0.20), residues: 1701 helix: -1.73 (0.31), residues: 245 sheet: -0.15 (0.31), residues: 304 loop : -1.87 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 414 HIS 0.011 0.002 HIS E 199 PHE 0.021 0.002 PHE F 89 TYR 0.025 0.002 TYR F 512 ARG 0.007 0.001 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 LEU cc_start: 0.8928 (tp) cc_final: 0.8719 (pt) REVERT: E 428 PHE cc_start: 0.9159 (m-10) cc_final: 0.8930 (m-10) REVERT: E 844 LEU cc_start: 0.9361 (mm) cc_final: 0.8655 (mm) REVERT: E 845 TYR cc_start: 0.8953 (m-80) cc_final: 0.8681 (m-80) REVERT: E 859 LEU cc_start: 0.9005 (tp) cc_final: 0.8683 (tt) REVERT: F 404 ASP cc_start: 0.8640 (m-30) cc_final: 0.8050 (t0) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2075 time to fit residues: 32.0967 Evaluate side-chains 68 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 93 optimal weight: 0.0270 chunk 120 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 163 optimal weight: 0.4980 chunk 102 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 263 HIS E 276 GLN E 407 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14356 Z= 0.155 Angle : 0.663 12.564 19457 Z= 0.328 Chirality : 0.047 0.210 2128 Planarity : 0.004 0.048 2511 Dihedral : 5.974 43.238 1899 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.88 % Favored : 91.83 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.96 (0.20), residues: 1701 helix: -1.45 (0.33), residues: 246 sheet: 0.10 (0.31), residues: 300 loop : -1.76 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 414 HIS 0.006 0.001 HIS E 247 PHE 0.030 0.002 PHE E 88 TYR 0.013 0.001 TYR G 14 ARG 0.006 0.000 ARG F 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 LEU cc_start: 0.9294 (tp) cc_final: 0.9070 (mt) REVERT: E 428 PHE cc_start: 0.9060 (m-10) cc_final: 0.8806 (m-10) REVERT: E 842 ILE cc_start: 0.8869 (pt) cc_final: 0.8663 (tp) REVERT: E 845 TYR cc_start: 0.8855 (m-80) cc_final: 0.8553 (m-80) REVERT: E 847 VAL cc_start: 0.9568 (t) cc_final: 0.9367 (t) REVERT: E 859 LEU cc_start: 0.9013 (tp) cc_final: 0.8622 (tt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2238 time to fit residues: 35.7378 Evaluate side-chains 77 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 128 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS E 407 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN F 858 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14356 Z= 0.187 Angle : 0.660 12.135 19457 Z= 0.328 Chirality : 0.046 0.287 2128 Planarity : 0.004 0.041 2511 Dihedral : 5.831 43.866 1899 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.17 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.20), residues: 1701 helix: -1.29 (0.33), residues: 240 sheet: 0.08 (0.31), residues: 304 loop : -1.73 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 414 HIS 0.006 0.001 HIS E 32 PHE 0.023 0.002 PHE E 89 TYR 0.021 0.001 TYR F 849 ARG 0.018 0.000 ARG F 850 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 428 PHE cc_start: 0.9079 (m-10) cc_final: 0.8835 (m-10) REVERT: E 842 ILE cc_start: 0.8868 (pt) cc_final: 0.8666 (tp) REVERT: E 845 TYR cc_start: 0.8826 (m-80) cc_final: 0.8452 (m-80) REVERT: E 859 LEU cc_start: 0.9083 (tp) cc_final: 0.8724 (tt) REVERT: F 535 ASP cc_start: 0.8861 (p0) cc_final: 0.8469 (t70) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2261 time to fit residues: 33.6212 Evaluate side-chains 74 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 HIS E 199 HIS ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 ASN ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 14356 Z= 0.476 Angle : 0.912 11.390 19457 Z= 0.460 Chirality : 0.051 0.237 2128 Planarity : 0.005 0.057 2511 Dihedral : 6.847 47.906 1899 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 33.30 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.29 % Favored : 87.36 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.37 (0.20), residues: 1701 helix: -1.58 (0.30), residues: 241 sheet: -0.51 (0.30), residues: 308 loop : -2.00 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 414 HIS 0.013 0.002 HIS E 199 PHE 0.028 0.003 PHE E 475 TYR 0.024 0.003 TYR B 16 ARG 0.014 0.001 ARG F 850 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 56 MET cc_start: 0.9398 (ppp) cc_final: 0.9142 (ppp) REVERT: E 61 LEU cc_start: 0.9013 (tp) cc_final: 0.8809 (pt) REVERT: E 844 LEU cc_start: 0.9255 (mm) cc_final: 0.8719 (mm) REVERT: E 845 TYR cc_start: 0.9088 (m-80) cc_final: 0.8676 (m-80) REVERT: E 859 LEU cc_start: 0.9084 (tp) cc_final: 0.8826 (tt) REVERT: F 404 ASP cc_start: 0.8707 (m-30) cc_final: 0.8065 (t0) REVERT: D 10 GLU cc_start: 0.9137 (mp0) cc_final: 0.8817 (pm20) REVERT: D 11 LEU cc_start: 0.9075 (mt) cc_final: 0.8428 (mt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2042 time to fit residues: 28.1916 Evaluate side-chains 64 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 112 optimal weight: 0.4980 chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 0.0870 chunk 134 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14356 Z= 0.177 Angle : 0.694 13.068 19457 Z= 0.344 Chirality : 0.048 0.279 2128 Planarity : 0.004 0.038 2511 Dihedral : 6.088 43.249 1899 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.52 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.06 (0.20), residues: 1701 helix: -1.32 (0.33), residues: 248 sheet: -0.05 (0.31), residues: 302 loop : -1.86 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 414 HIS 0.005 0.001 HIS E 247 PHE 0.022 0.002 PHE E 89 TYR 0.015 0.001 TYR F 845 ARG 0.011 0.001 ARG F 850 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 MET cc_start: 0.9243 (ppp) cc_final: 0.9029 (ppp) REVERT: E 109 LEU cc_start: 0.8981 (mt) cc_final: 0.8728 (mt) REVERT: E 428 PHE cc_start: 0.9032 (m-10) cc_final: 0.8820 (m-10) REVERT: E 842 ILE cc_start: 0.8831 (pt) cc_final: 0.8572 (tp) REVERT: E 845 TYR cc_start: 0.8952 (m-80) cc_final: 0.8663 (m-80) REVERT: E 859 LEU cc_start: 0.9077 (tp) cc_final: 0.8806 (tt) REVERT: D 10 GLU cc_start: 0.9155 (mp0) cc_final: 0.8858 (pm20) REVERT: D 11 LEU cc_start: 0.9083 (mt) cc_final: 0.8438 (mt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2329 time to fit residues: 34.5344 Evaluate side-chains 74 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.066918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.051876 restraints weight = 109394.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.051135 restraints weight = 70282.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.051483 restraints weight = 61897.363| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14356 Z= 0.268 Angle : 0.716 12.032 19457 Z= 0.358 Chirality : 0.047 0.238 2128 Planarity : 0.004 0.037 2511 Dihedral : 6.149 46.414 1899 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.35 % Favored : 88.36 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1701 helix: -1.37 (0.32), residues: 251 sheet: -0.13 (0.31), residues: 302 loop : -1.88 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 414 HIS 0.005 0.001 HIS F 1 PHE 0.015 0.002 PHE E 89 TYR 0.013 0.002 TYR F 579 ARG 0.011 0.001 ARG F 850 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.83 seconds wall clock time: 42 minutes 36.55 seconds (2556.55 seconds total)