Starting phenix.real_space_refine on Fri Feb 16 20:35:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jkq_22367/02_2024/7jkq_22367.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jkq_22367/02_2024/7jkq_22367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jkq_22367/02_2024/7jkq_22367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jkq_22367/02_2024/7jkq_22367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jkq_22367/02_2024/7jkq_22367.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jkq_22367/02_2024/7jkq_22367.pdb" } resolution = 3.3 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= 0.001 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 65 5.16 5 C 10577 2.51 5 N 2776 2.21 5 O 3019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 19": "OD1" <-> "OD2" Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A ASP 281": "OD1" <-> "OD2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A ASP 301": "OD1" <-> "OD2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 581": "OD1" <-> "OD2" Residue "A ASP 582": "OD1" <-> "OD2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A ASP 704": "OD1" <-> "OD2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 763": "OD1" <-> "OD2" Residue "A GLU 775": "OE1" <-> "OE2" Residue "A TYR 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "A TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 32": "OD1" <-> "OD2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "D PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D GLU 296": "OE1" <-> "OE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 394": "OE1" <-> "OE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D GLU 415": "OE1" <-> "OE2" Residue "D ASP 425": "OD1" <-> "OD2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 618": "OD1" <-> "OD2" Residue "D TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D GLU 703": "OE1" <-> "OE2" Residue "D GLU 707": "OE1" <-> "OE2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 763": "OD1" <-> "OD2" Residue "D TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 768": "OE1" <-> "OE2" Residue "D GLU 775": "OE1" <-> "OE2" Residue "D GLU 791": "OE1" <-> "OE2" Residue "D TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 849": "OE1" <-> "OE2" Residue "D PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16437 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6650 Classifications: {'peptide': 827} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 772} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2153 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 252} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1023 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 12, 'TRANS': 114} Chain: "D" Number of atoms: 6611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 6611 Classifications: {'peptide': 822} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 53, 'TRANS': 768} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 9.15, per 1000 atoms: 0.56 Number of scatterers: 16437 At special positions: 0 Unit cell: (112.2, 117.15, 149.325, 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 65 16.00 O 3019 8.00 N 2776 7.00 C 10577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 6.29 Conformation dependent library (CDL) restraints added in 2.8 seconds 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3834 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 30 sheets defined 18.9% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 19 through 23 removed outlier: 4.106A pdb=" N ALA A 22 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 23 " --> pdb=" O PRO A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 23' Processing helix chain 'A' and resid 30 through 42 Processing helix chain 'A' and resid 44 through 49 removed outlier: 3.617A pdb=" N VAL A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 583 through 587 removed outlier: 3.526A pdb=" N HIS A 586 " --> pdb=" O ASP A 583 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 587 " --> pdb=" O PRO A 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 583 through 587' Processing helix chain 'A' and resid 661 through 671 removed outlier: 3.728A pdb=" N ASN A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 700 through 716 Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 763 through 771 removed outlier: 3.926A pdb=" N ARG A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 Processing helix chain 'A' and resid 786 through 793 removed outlier: 4.181A pdb=" N VAL A 790 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLU A 791 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 827 removed outlier: 4.141A pdb=" N THR A 816 " --> pdb=" O HIS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 863 Processing helix chain 'B' and resid 213 through 218 removed outlier: 3.811A pdb=" N HIS B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.920A pdb=" N LEU B 320 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE B 321 " --> pdb=" O ASN B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 317 through 321' Processing helix chain 'B' and resid 348 through 360 Processing helix chain 'C' and resid 350 through 359 removed outlier: 3.926A pdb=" N PHE C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.889A pdb=" N ARG D 23 " --> pdb=" O PRO D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 42 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 583 through 587 Processing helix chain 'D' and resid 661 through 671 removed outlier: 3.729A pdb=" N ASN D 665 " --> pdb=" O TYR D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 691 Processing helix chain 'D' and resid 692 through 694 No H-bonds generated for 'chain 'D' and resid 692 through 694' Processing helix chain 'D' and resid 700 through 716 Processing helix chain 'D' and resid 730 through 743 Processing helix chain 'D' and resid 763 through 771 removed outlier: 3.974A pdb=" N ARG D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR D 770 " --> pdb=" O TYR D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 785 Processing helix chain 'D' and resid 786 through 793 removed outlier: 4.081A pdb=" N VAL D 790 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU D 791 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 827 removed outlier: 4.295A pdb=" N THR D 816 " --> pdb=" O HIS D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 863 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 60 removed outlier: 5.975A pdb=" N ASP A 55 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU A 75 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 4.834A pdb=" N LEU A 159 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 193 removed outlier: 6.629A pdb=" N SER A 202 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ILE A 193 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE A 200 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 239 Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 239 removed outlier: 8.980A pdb=" N LEU A 317 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 338 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A 332 " --> pdb=" O GLN A 323 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 287 through 291 Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 357 removed outlier: 6.803A pdb=" N MET A 367 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA A 355 " --> pdb=" O TRP A 365 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP A 365 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR A 413 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU A 380 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL A 411 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 445 removed outlier: 3.616A pdb=" N HIS A 453 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 496 through 497 removed outlier: 4.817A pdb=" N GLN A 516 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 496 through 497 removed outlier: 4.817A pdb=" N GLN A 516 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 547 through 552 removed outlier: 6.622A pdb=" N VAL A 572 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LYS A 576 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N PHE A 591 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER A 578 " --> pdb=" O PRO A 589 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 609 through 614 removed outlier: 4.107A pdb=" N TYR A 622 " --> pdb=" O ASP A 678 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 677 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N HIS A 637 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG A 723 " --> pdb=" O HIS A 637 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TRP A 729 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 749 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 724 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE A 751 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 726 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLY A 753 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLY A 728 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA A 750 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU A 803 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA A 752 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N GLY A 805 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 171 through 174 removed outlier: 7.039A pdb=" N ARG B 179 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 236 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 234 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AB7, first strand: chain 'B' and resid 326 through 334 removed outlier: 3.834A pdb=" N LYS B 345 " --> pdb=" O HIS B 326 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 396 through 398 Processing sheet with id=AB9, first strand: chain 'C' and resid 326 through 332 Processing sheet with id=AC1, first strand: chain 'C' and resid 396 through 399 removed outlier: 4.165A pdb=" N ALA C 380 " --> pdb=" O ILE C 399 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG C 422 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU C 439 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY C 424 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU C 437 " --> pdb=" O GLY C 424 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 426 " --> pdb=" O VAL C 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.612A pdb=" N HIS D 70 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D 74 " --> pdb=" O LEU D 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 140 through 145 removed outlier: 6.337A pdb=" N SER D 141 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLN D 154 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 188 through 193 removed outlier: 6.597A pdb=" N SER D 202 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE D 193 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N PHE D 200 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 237 through 239 Processing sheet with id=AC6, first strand: chain 'D' and resid 237 through 239 removed outlier: 3.520A pdb=" N PHE D 322 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N LEU D 317 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU D 338 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER D 332 " --> pdb=" O GLN D 323 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 287 through 291 Processing sheet with id=AC8, first strand: chain 'D' and resid 351 through 355 removed outlier: 5.482A pdb=" N ILE D 352 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU D 369 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG D 354 " --> pdb=" O MET D 367 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR D 413 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU D 380 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL D 411 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 427 through 429 removed outlier: 3.735A pdb=" N HIS D 453 " --> pdb=" O ASN D 445 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU D 454 " --> pdb=" O ALA D 488 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA D 488 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LYS D 456 " --> pdb=" O GLU D 486 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU D 486 " --> pdb=" O LYS D 456 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR D 458 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 505 through 507 Processing sheet with id=AD2, first strand: chain 'D' and resid 547 through 552 removed outlier: 6.767A pdb=" N VAL D 572 " --> pdb=" O MET D 595 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LYS D 576 " --> pdb=" O PHE D 591 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE D 591 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER D 578 " --> pdb=" O PRO D 589 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 609 through 614 removed outlier: 4.213A pdb=" N TYR D 622 " --> pdb=" O ASP D 678 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE D 677 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N HIS D 637 " --> pdb=" O LEU D 721 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG D 723 " --> pdb=" O HIS D 637 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TRP D 729 " --> pdb=" O VAL D 643 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL D 749 " --> pdb=" O SER D 722 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL D 724 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE D 751 " --> pdb=" O VAL D 724 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE D 726 " --> pdb=" O ILE D 751 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY D 753 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLY D 728 " --> pdb=" O GLY D 753 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA D 750 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU D 803 " --> pdb=" O ALA D 750 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA D 752 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N GLY D 805 " --> pdb=" O ALA D 752 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.38 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4975 1.34 - 1.46: 3760 1.46 - 1.58: 8097 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 16934 Sorted by residual: bond pdb=" CB MET D 558 " pdb=" CG MET D 558 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.99e+00 bond pdb=" N PRO B 363 " pdb=" CA PRO B 363 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.40e-02 5.10e+03 4.85e+00 bond pdb=" CG LEU D 369 " pdb=" CD2 LEU D 369 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.43e+00 bond pdb=" CB VAL A 786 " pdb=" CG2 VAL A 786 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.01e+00 bond pdb=" CB VAL A 786 " pdb=" CG1 VAL A 786 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.94e+00 ... (remaining 16929 not shown) Histogram of bond angle deviations from ideal: 97.72 - 105.03: 439 105.03 - 112.34: 7847 112.34 - 119.65: 6162 119.65 - 126.95: 8255 126.95 - 134.26: 316 Bond angle restraints: 23019 Sorted by residual: angle pdb=" N LYS D 336 " pdb=" CA LYS D 336 " pdb=" CB LYS D 336 " ideal model delta sigma weight residual 111.37 99.77 11.60 1.82e+00 3.02e-01 4.06e+01 angle pdb=" CA LYS D 336 " pdb=" CB LYS D 336 " pdb=" CG LYS D 336 " ideal model delta sigma weight residual 114.10 126.26 -12.16 2.00e+00 2.50e-01 3.69e+01 angle pdb=" CB ARG A 354 " pdb=" CG ARG A 354 " pdb=" CD ARG A 354 " ideal model delta sigma weight residual 111.30 124.00 -12.70 2.30e+00 1.89e-01 3.05e+01 angle pdb=" C MET D 189 " pdb=" N ASP D 190 " pdb=" CA ASP D 190 " ideal model delta sigma weight residual 122.83 128.25 -5.42 1.08e+00 8.57e-01 2.52e+01 angle pdb=" CB MET A 558 " pdb=" CG MET A 558 " pdb=" SD MET A 558 " ideal model delta sigma weight residual 112.70 98.61 14.09 3.00e+00 1.11e-01 2.20e+01 ... (remaining 23014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8992 17.99 - 35.97: 814 35.97 - 53.96: 150 53.96 - 71.94: 35 71.94 - 89.93: 16 Dihedral angle restraints: 10007 sinusoidal: 4041 harmonic: 5966 Sorted by residual: dihedral pdb=" CA TRP D 729 " pdb=" C TRP D 729 " pdb=" N SER D 730 " pdb=" CA SER D 730 " ideal model delta harmonic sigma weight residual -180.00 -123.85 -56.15 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA TRP A 729 " pdb=" C TRP A 729 " pdb=" N SER A 730 " pdb=" CA SER A 730 " ideal model delta harmonic sigma weight residual -180.00 -124.38 -55.62 0 5.00e+00 4.00e-02 1.24e+02 dihedral pdb=" CA ALA A 599 " pdb=" C ALA A 599 " pdb=" N SER A 600 " pdb=" CA SER A 600 " ideal model delta harmonic sigma weight residual -180.00 -146.61 -33.39 0 5.00e+00 4.00e-02 4.46e+01 ... (remaining 10004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2295 0.139 - 0.278: 128 0.278 - 0.416: 5 0.416 - 0.555: 0 0.555 - 0.694: 2 Chirality restraints: 2430 Sorted by residual: chirality pdb=" CG LEU A 803 " pdb=" CB LEU A 803 " pdb=" CD1 LEU A 803 " pdb=" CD2 LEU A 803 " both_signs ideal model delta sigma weight residual False -2.59 -1.90 -0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CG LEU D 664 " pdb=" CB LEU D 664 " pdb=" CD1 LEU D 664 " pdb=" CD2 LEU D 664 " both_signs ideal model delta sigma weight residual False -2.59 -2.02 -0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" CB ILE B 418 " pdb=" CA ILE B 418 " pdb=" CG1 ILE B 418 " pdb=" CG2 ILE B 418 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2427 not shown) Planarity restraints: 2987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 197 " 0.100 5.00e-02 4.00e+02 1.49e-01 3.54e+01 pdb=" N PRO D 198 " -0.257 5.00e-02 4.00e+02 pdb=" CA PRO D 198 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO D 198 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 393 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C GLU D 393 " -0.075 2.00e-02 2.50e+03 pdb=" O GLU D 393 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU D 394 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 543 " -0.061 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO D 544 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO D 544 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 544 " -0.050 5.00e-02 4.00e+02 ... (remaining 2984 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2690 2.77 - 3.30: 14942 3.30 - 3.84: 28462 3.84 - 4.37: 33023 4.37 - 4.90: 56837 Nonbonded interactions: 135954 Sorted by model distance: nonbonded pdb=" O GLY B 259 " pdb=" OH TYR B 322 " model vdw 2.238 2.440 nonbonded pdb=" OH TYR A 466 " pdb=" OE1 GLU A 478 " model vdw 2.252 2.440 nonbonded pdb=" OD2 ASP B 262 " pdb=" OG SER B 264 " model vdw 2.262 2.440 nonbonded pdb=" OG SER D 207 " pdb=" OG SER D 238 " model vdw 2.263 2.440 nonbonded pdb=" OG SER A 158 " pdb=" OE2 GLU A 179 " model vdw 2.284 2.440 ... (remaining 135949 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 18 through 114 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 863)) selection = chain 'D' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.630 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: 13.570 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 45.650 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.007 0.077 16934 Z= 0.435 Angle : 1.219 15.962 23019 Z= 0.659 Chirality : 0.071 0.694 2430 Planarity : 0.009 0.149 2987 Dihedral : 14.736 89.926 6173 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.19 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.72 % Twisted General : 0.21 % 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: -3.03 (0.16), residues: 2034 helix: -1.57 (0.25), residues: 304 sheet: -2.17 (0.18), residues: 618 loop : -2.02 (0.16), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP D 258 HIS 0.018 0.002 HIS A 70 PHE 0.044 0.004 PHE B 332 TYR 0.050 0.003 TYR D 563 ARG 0.014 0.001 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.8125 (mmm) cc_final: 0.7783 (mtp) REVERT: A 350 GLU cc_start: 0.6878 (tp30) cc_final: 0.6575 (tp30) REVERT: A 401 ARG cc_start: 0.7685 (mmt90) cc_final: 0.7317 (mmm-85) REVERT: A 772 ASP cc_start: 0.6596 (m-30) cc_final: 0.6372 (m-30) REVERT: A 773 VAL cc_start: 0.7259 (t) cc_final: 0.6946 (t) REVERT: B 189 TRP cc_start: 0.7262 (t-100) cc_final: 0.7028 (t-100) REVERT: B 372 SER cc_start: 0.7779 (m) cc_final: 0.7313 (p) REVERT: C 427 VAL cc_start: 0.6952 (t) cc_final: 0.6638 (m) REVERT: D 42 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.6981 (mtt90) REVERT: D 91 ILE cc_start: 0.8175 (mm) cc_final: 0.7943 (pt) REVERT: D 108 MET cc_start: 0.6762 (tpt) cc_final: 0.5813 (tmm) REVERT: D 468 TRP cc_start: 0.7567 (m100) cc_final: 0.7337 (m100) REVERT: D 809 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6861 (mt-10) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.3118 time to fit residues: 190.7160 Evaluate side-chains 280 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 629 HIS A 798 ASN A 860 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 GLN D 516 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 GLN D 840 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16934 Z= 0.257 Angle : 0.655 9.664 23019 Z= 0.339 Chirality : 0.047 0.227 2430 Planarity : 0.006 0.089 2987 Dihedral : 6.038 45.008 2218 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.68 % Allowed : 9.97 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.17), residues: 2034 helix: -0.12 (0.28), residues: 316 sheet: -1.60 (0.19), residues: 610 loop : -1.75 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 375 HIS 0.007 0.001 HIS A 804 PHE 0.016 0.001 PHE B 253 TYR 0.027 0.002 TYR B 322 ARG 0.009 0.001 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 308 time to evaluate : 1.846 Fit side-chains REVERT: A 154 GLN cc_start: 0.8084 (tt0) cc_final: 0.7841 (tt0) REVERT: A 189 MET cc_start: 0.8225 (mmm) cc_final: 0.7984 (mtm) REVERT: A 190 ASP cc_start: 0.7926 (t70) cc_final: 0.7709 (t70) REVERT: A 604 ASP cc_start: 0.6824 (t0) cc_final: 0.6597 (t0) REVERT: A 772 ASP cc_start: 0.6574 (m-30) cc_final: 0.6248 (m-30) REVERT: B 220 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7756 (tt) REVERT: B 328 GLU cc_start: 0.5057 (pp20) cc_final: 0.3658 (tp30) REVERT: B 345 LYS cc_start: 0.6766 (mmmt) cc_final: 0.5917 (mmmt) REVERT: B 372 SER cc_start: 0.7892 (m) cc_final: 0.7411 (p) REVERT: C 427 VAL cc_start: 0.6955 (t) cc_final: 0.6614 (m) REVERT: D 42 ARG cc_start: 0.7067 (mtm-85) cc_final: 0.6689 (mtt90) REVERT: D 108 MET cc_start: 0.6421 (tpt) cc_final: 0.5785 (tmm) REVERT: D 314 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7503 (mtpp) REVERT: D 468 TRP cc_start: 0.7672 (m100) cc_final: 0.7355 (m100) REVERT: D 482 PRO cc_start: 0.7911 (Cg_endo) cc_final: 0.7672 (Cg_exo) REVERT: D 661 TYR cc_start: 0.8479 (m-80) cc_final: 0.8094 (m-80) outliers start: 30 outliers final: 21 residues processed: 324 average time/residue: 0.3055 time to fit residues: 145.6210 Evaluate side-chains 296 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 273 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 665 ASN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 551 SER Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 153 optimal weight: 0.3980 chunk 125 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 199 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN A 837 ASN A 840 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 GLN D 525 HIS D 573 HIS D 840 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16934 Z= 0.187 Angle : 0.601 8.152 23019 Z= 0.308 Chirality : 0.045 0.202 2430 Planarity : 0.005 0.068 2987 Dihedral : 5.596 41.732 2218 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.24 % Allowed : 12.54 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.72 (0.18), residues: 2034 helix: 0.42 (0.30), residues: 316 sheet: -1.19 (0.20), residues: 606 loop : -1.57 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 375 HIS 0.005 0.001 HIS A 804 PHE 0.014 0.001 PHE B 253 TYR 0.023 0.002 TYR B 322 ARG 0.009 0.000 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 296 time to evaluate : 2.015 Fit side-chains REVERT: A 464 GLN cc_start: 0.7302 (tm-30) cc_final: 0.6693 (tm-30) REVERT: A 595 MET cc_start: 0.8305 (mmm) cc_final: 0.8091 (mtp) REVERT: A 604 ASP cc_start: 0.7058 (t0) cc_final: 0.6815 (t0) REVERT: A 772 ASP cc_start: 0.6617 (m-30) cc_final: 0.6309 (m-30) REVERT: A 844 CYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7853 (t) REVERT: B 190 TYR cc_start: 0.6504 (m-10) cc_final: 0.6215 (m-10) REVERT: B 272 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7736 (mmtt) REVERT: B 334 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.4969 (tt) REVERT: B 372 SER cc_start: 0.7901 (m) cc_final: 0.7409 (p) REVERT: D 42 ARG cc_start: 0.7104 (mtm-85) cc_final: 0.6834 (mtt90) REVERT: D 108 MET cc_start: 0.6432 (tpt) cc_final: 0.5759 (tmm) REVERT: D 375 TRP cc_start: 0.7824 (t60) cc_final: 0.7444 (t60) REVERT: D 468 TRP cc_start: 0.7584 (m100) cc_final: 0.7348 (m100) REVERT: D 817 ASN cc_start: 0.8885 (m-40) cc_final: 0.8663 (m-40) outliers start: 40 outliers final: 23 residues processed: 320 average time/residue: 0.2986 time to fit residues: 142.4495 Evaluate side-chains 294 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 269 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 355 HIS Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 551 SER Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 786 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 124 optimal weight: 4.9990 chunk 185 optimal weight: 0.0980 chunk 196 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 ASN A 840 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 ASN D 840 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16934 Z= 0.185 Angle : 0.575 8.619 23019 Z= 0.295 Chirality : 0.044 0.207 2430 Planarity : 0.005 0.071 2987 Dihedral : 5.330 38.324 2218 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.19 % Allowed : 12.71 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.42 (0.18), residues: 2034 helix: 0.73 (0.31), residues: 310 sheet: -0.91 (0.21), residues: 600 loop : -1.45 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 375 HIS 0.005 0.001 HIS A 804 PHE 0.027 0.001 PHE D 427 TYR 0.023 0.001 TYR B 322 ARG 0.009 0.000 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 293 time to evaluate : 1.776 Fit side-chains revert: symmetry clash REVERT: A 350 GLU cc_start: 0.7678 (tp30) cc_final: 0.7428 (tp30) REVERT: A 772 ASP cc_start: 0.6509 (m-30) cc_final: 0.6262 (m-30) REVERT: A 844 CYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7836 (t) REVERT: B 334 LEU cc_start: 0.5483 (OUTLIER) cc_final: 0.4955 (tt) REVERT: B 372 SER cc_start: 0.7848 (m) cc_final: 0.7359 (p) REVERT: D 42 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.6849 (mtt90) REVERT: D 108 MET cc_start: 0.6463 (tpt) cc_final: 0.5759 (tmm) REVERT: D 222 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8878 (mt) REVERT: D 375 TRP cc_start: 0.7809 (t60) cc_final: 0.7441 (t60) REVERT: D 468 TRP cc_start: 0.7576 (m100) cc_final: 0.7363 (m100) REVERT: D 660 LYS cc_start: 0.7803 (pptt) cc_final: 0.7424 (pttt) REVERT: D 817 ASN cc_start: 0.8889 (m-40) cc_final: 0.8673 (m-40) outliers start: 57 outliers final: 35 residues processed: 330 average time/residue: 0.2907 time to fit residues: 143.7872 Evaluate side-chains 304 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 266 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 844 CYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 551 SER Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 624 MET Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN A 812 HIS A 840 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 GLN ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 GLN D 840 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 16934 Z= 0.574 Angle : 0.750 11.718 23019 Z= 0.386 Chirality : 0.050 0.310 2430 Planarity : 0.006 0.069 2987 Dihedral : 5.875 37.983 2218 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.09 % Allowed : 14.05 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.76 (0.18), residues: 2034 helix: 0.00 (0.29), residues: 322 sheet: -1.15 (0.20), residues: 641 loop : -1.51 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP A 258 HIS 0.011 0.002 HIS A 804 PHE 0.022 0.002 PHE B 253 TYR 0.026 0.003 TYR B 322 ARG 0.012 0.001 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 277 time to evaluate : 1.906 Fit side-chains REVERT: A 39 HIS cc_start: 0.7374 (OUTLIER) cc_final: 0.6879 (t-90) REVERT: A 151 PHE cc_start: 0.8930 (m-80) cc_final: 0.8675 (m-80) REVERT: A 350 GLU cc_start: 0.7956 (tp30) cc_final: 0.7743 (tp30) REVERT: A 803 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9067 (mm) REVERT: B 190 TYR cc_start: 0.6550 (m-10) cc_final: 0.6174 (m-10) REVERT: B 220 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7930 (tt) REVERT: B 334 LEU cc_start: 0.5646 (OUTLIER) cc_final: 0.5191 (tt) REVERT: C 427 VAL cc_start: 0.6986 (t) cc_final: 0.6454 (m) REVERT: D 42 ARG cc_start: 0.7177 (mtm-85) cc_final: 0.6968 (mtt90) REVERT: D 108 MET cc_start: 0.6363 (tpt) cc_final: 0.5769 (tmm) REVERT: D 181 LYS cc_start: 0.7978 (tptp) cc_final: 0.7543 (mmmt) REVERT: D 314 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7488 (mtpp) REVERT: D 575 TYR cc_start: 0.7716 (m-10) cc_final: 0.7403 (m-80) REVERT: D 660 LYS cc_start: 0.8054 (pptt) cc_final: 0.7815 (pttt) REVERT: D 771 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7129 (mmm) outliers start: 73 outliers final: 43 residues processed: 327 average time/residue: 0.3109 time to fit residues: 148.4921 Evaluate side-chains 312 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 263 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 551 SER Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 678 ASP Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 834 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 196 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 HIS ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16934 Z= 0.233 Angle : 0.616 10.314 23019 Z= 0.316 Chirality : 0.045 0.227 2430 Planarity : 0.005 0.060 2987 Dihedral : 5.510 36.650 2218 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.74 % Allowed : 16.46 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.48 (0.18), residues: 2034 helix: 0.45 (0.30), residues: 317 sheet: -0.89 (0.21), residues: 599 loop : -1.45 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 375 HIS 0.012 0.001 HIS D 161 PHE 0.018 0.001 PHE D 427 TYR 0.023 0.002 TYR A 363 ARG 0.013 0.000 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 295 time to evaluate : 1.991 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7084 (OUTLIER) cc_final: 0.6780 (t-90) REVERT: A 175 MET cc_start: 0.8035 (pmm) cc_final: 0.7319 (ptp) REVERT: A 270 LEU cc_start: 0.7175 (mm) cc_final: 0.6921 (mt) REVERT: A 350 GLU cc_start: 0.7891 (tp30) cc_final: 0.7663 (tp30) REVERT: B 222 LEU cc_start: 0.8383 (mt) cc_final: 0.8046 (mt) REVERT: B 334 LEU cc_start: 0.5553 (OUTLIER) cc_final: 0.5105 (tt) REVERT: B 372 SER cc_start: 0.7909 (m) cc_final: 0.7369 (p) REVERT: D 108 MET cc_start: 0.6350 (tpt) cc_final: 0.5699 (tmm) REVERT: D 181 LYS cc_start: 0.7928 (tptp) cc_final: 0.7533 (mmmt) REVERT: D 314 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7494 (mtpp) REVERT: D 468 TRP cc_start: 0.7705 (m100) cc_final: 0.7400 (m100) REVERT: D 575 TYR cc_start: 0.7627 (m-10) cc_final: 0.7349 (m-80) REVERT: D 660 LYS cc_start: 0.7962 (pptt) cc_final: 0.7621 (pttt) REVERT: D 771 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.6932 (mmm) outliers start: 49 outliers final: 32 residues processed: 326 average time/residue: 0.3166 time to fit residues: 151.0370 Evaluate side-chains 309 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 273 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 551 SER Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN A 684 GLN A 798 ASN A 840 HIS B 270 HIS ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16934 Z= 0.287 Angle : 0.627 11.315 23019 Z= 0.320 Chirality : 0.046 0.234 2430 Planarity : 0.005 0.069 2987 Dihedral : 5.406 35.476 2218 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.58 % Allowed : 16.74 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.41 (0.18), residues: 2034 helix: 0.50 (0.30), residues: 316 sheet: -0.90 (0.21), residues: 609 loop : -1.37 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 375 HIS 0.010 0.001 HIS D 70 PHE 0.016 0.001 PHE B 253 TYR 0.023 0.002 TYR B 322 ARG 0.013 0.001 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 275 time to evaluate : 2.064 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6849 (t-90) REVERT: A 151 PHE cc_start: 0.8885 (m-80) cc_final: 0.8667 (m-80) REVERT: A 175 MET cc_start: 0.8021 (pmm) cc_final: 0.7344 (ptp) REVERT: A 350 GLU cc_start: 0.7927 (tp30) cc_final: 0.7727 (tp30) REVERT: B 227 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: B 334 LEU cc_start: 0.5568 (OUTLIER) cc_final: 0.5130 (tt) REVERT: D 181 LYS cc_start: 0.7934 (tptp) cc_final: 0.7535 (mmmt) REVERT: D 314 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7529 (mtpp) REVERT: D 468 TRP cc_start: 0.7643 (m100) cc_final: 0.7329 (m100) REVERT: D 575 TYR cc_start: 0.7613 (m-10) cc_final: 0.7326 (m-80) REVERT: D 576 LYS cc_start: 0.8645 (tptm) cc_final: 0.8363 (tptp) REVERT: D 660 LYS cc_start: 0.8003 (pttt) cc_final: 0.7698 (pttt) REVERT: D 771 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.6998 (mmm) outliers start: 64 outliers final: 41 residues processed: 321 average time/residue: 0.3191 time to fit residues: 148.7886 Evaluate side-chains 317 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 271 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 551 SER Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 841 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.0050 chunk 124 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 ASN A 798 ASN A 840 HIS ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16934 Z= 0.214 Angle : 0.616 10.184 23019 Z= 0.312 Chirality : 0.045 0.216 2430 Planarity : 0.005 0.061 2987 Dihedral : 5.279 34.665 2218 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.91 % Allowed : 17.53 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.33 (0.18), residues: 2034 helix: 0.59 (0.30), residues: 317 sheet: -0.77 (0.21), residues: 607 loop : -1.38 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 375 HIS 0.008 0.001 HIS D 161 PHE 0.014 0.001 PHE D 427 TYR 0.022 0.002 TYR A 277 ARG 0.014 0.001 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 283 time to evaluate : 1.850 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6738 (t-90) REVERT: A 175 MET cc_start: 0.7996 (pmm) cc_final: 0.7441 (ptp) REVERT: A 378 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8296 (tt) REVERT: B 208 THR cc_start: 0.6966 (m) cc_final: 0.6723 (p) REVERT: B 220 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7906 (tt) REVERT: B 227 GLN cc_start: 0.7837 (mp10) cc_final: 0.7306 (mp10) REVERT: B 334 LEU cc_start: 0.5590 (OUTLIER) cc_final: 0.5142 (tt) REVERT: D 108 MET cc_start: 0.6819 (tmm) cc_final: 0.6222 (tmm) REVERT: D 171 MET cc_start: 0.2104 (ppp) cc_final: 0.1880 (ppp) REVERT: D 181 LYS cc_start: 0.7923 (tptp) cc_final: 0.7521 (mmmt) REVERT: D 314 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7547 (mtpp) REVERT: D 468 TRP cc_start: 0.7571 (m100) cc_final: 0.7314 (m100) REVERT: D 575 TYR cc_start: 0.7517 (m-10) cc_final: 0.7223 (m-80) REVERT: D 576 LYS cc_start: 0.8612 (tptm) cc_final: 0.8387 (tptp) REVERT: D 660 LYS cc_start: 0.7933 (pttt) cc_final: 0.7635 (pttt) REVERT: D 771 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.6959 (mmm) outliers start: 52 outliers final: 41 residues processed: 317 average time/residue: 0.3132 time to fit residues: 144.4509 Evaluate side-chains 308 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 261 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 551 SER Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 841 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 181 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 798 ASN A 840 HIS ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 GLN D 665 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16934 Z= 0.242 Angle : 0.618 10.381 23019 Z= 0.314 Chirality : 0.045 0.221 2430 Planarity : 0.005 0.064 2987 Dihedral : 5.245 34.265 2218 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.36 % Allowed : 17.08 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.26 (0.18), residues: 2034 helix: 0.66 (0.30), residues: 316 sheet: -0.75 (0.21), residues: 604 loop : -1.33 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.002 TRP A 375 HIS 0.007 0.001 HIS D 161 PHE 0.015 0.001 PHE B 253 TYR 0.022 0.002 TYR B 322 ARG 0.014 0.000 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 277 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6773 (t-90) REVERT: A 175 MET cc_start: 0.8009 (pmm) cc_final: 0.7444 (ptp) REVERT: A 378 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8281 (tt) REVERT: B 208 THR cc_start: 0.7025 (m) cc_final: 0.6779 (p) REVERT: B 220 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7929 (tt) REVERT: B 227 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: B 334 LEU cc_start: 0.5616 (OUTLIER) cc_final: 0.5191 (tt) REVERT: D 57 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8067 (mm-40) REVERT: D 171 MET cc_start: 0.2194 (ppp) cc_final: 0.1878 (ppp) REVERT: D 181 LYS cc_start: 0.7922 (tptp) cc_final: 0.7524 (mmmt) REVERT: D 314 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7561 (mtpp) REVERT: D 468 TRP cc_start: 0.7564 (m100) cc_final: 0.7297 (m100) REVERT: D 575 TYR cc_start: 0.7457 (m-10) cc_final: 0.7130 (m-80) REVERT: D 660 LYS cc_start: 0.7931 (pttt) cc_final: 0.7634 (pttt) REVERT: D 771 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.6975 (mmm) outliers start: 60 outliers final: 45 residues processed: 315 average time/residue: 0.3236 time to fit residues: 148.6105 Evaluate side-chains 323 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 271 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 551 SER Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 841 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 chunk 91 optimal weight: 0.2980 chunk 134 optimal weight: 0.3980 chunk 202 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 798 ASN A 840 HIS ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 GLN D 665 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16934 Z= 0.201 Angle : 0.612 9.443 23019 Z= 0.310 Chirality : 0.045 0.205 2430 Planarity : 0.005 0.057 2987 Dihedral : 5.162 33.634 2218 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.86 % Allowed : 17.58 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.19 (0.19), residues: 2034 helix: 0.76 (0.30), residues: 316 sheet: -0.69 (0.21), residues: 606 loop : -1.30 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP A 375 HIS 0.007 0.001 HIS D 161 PHE 0.014 0.001 PHE D 342 TYR 0.022 0.001 TYR A 277 ARG 0.015 0.000 ARG D 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 291 time to evaluate : 1.824 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7152 (OUTLIER) cc_final: 0.6803 (t-90) REVERT: A 175 MET cc_start: 0.7968 (pmm) cc_final: 0.7345 (ptp) REVERT: A 378 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8256 (tt) REVERT: B 208 THR cc_start: 0.7076 (m) cc_final: 0.6831 (p) REVERT: B 220 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7895 (tt) REVERT: B 227 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7289 (mp10) REVERT: B 334 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5076 (tt) REVERT: D 57 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8058 (mm-40) REVERT: D 171 MET cc_start: 0.2170 (ppp) cc_final: 0.1773 (ppp) REVERT: D 181 LYS cc_start: 0.7951 (tptp) cc_final: 0.7537 (mmmt) REVERT: D 314 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7590 (mtpp) REVERT: D 468 TRP cc_start: 0.7520 (m100) cc_final: 0.7307 (m100) REVERT: D 575 TYR cc_start: 0.7418 (m-10) cc_final: 0.7118 (m-80) REVERT: D 771 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7812 (mtt) outliers start: 51 outliers final: 37 residues processed: 320 average time/residue: 0.3039 time to fit residues: 142.3561 Evaluate side-chains 324 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 280 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 551 SER Chi-restraints excluded: chain D residue 554 GLN Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 771 MET Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 841 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 148 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 141 optimal weight: 0.0870 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 798 ASN A 840 HIS ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN D 648 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.180571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.130711 restraints weight = 22233.611| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.29 r_work: 0.3259 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16934 Z= 0.195 Angle : 0.610 9.488 23019 Z= 0.306 Chirality : 0.044 0.207 2430 Planarity : 0.005 0.061 2987 Dihedral : 5.082 33.347 2218 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.74 % Allowed : 18.37 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.13 (0.19), residues: 2034 helix: 0.83 (0.31), residues: 316 sheet: -0.63 (0.21), residues: 602 loop : -1.28 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.002 TRP A 375 HIS 0.006 0.001 HIS D 161 PHE 0.014 0.001 PHE B 253 TYR 0.022 0.001 TYR A 277 ARG 0.015 0.000 ARG D 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4403.39 seconds wall clock time: 80 minutes 9.22 seconds (4809.22 seconds total)