Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 14 16:02:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jkq_22367/08_2023/7jkq_22367.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jkq_22367/08_2023/7jkq_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_22367/08_2023/7jkq_22367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jkq_22367/08_2023/7jkq_22367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jkq_22367/08_2023/7jkq_22367.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jkq_22367/08_2023/7jkq_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-1.21rc1-5044/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: 7.18, per 1000 atoms: 0.44 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: 6.69 Conformation dependent library (CDL) restraints added in 2.5 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: 1.96 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: 6.84 Time building geometry restraints manager: 7.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 6.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.120 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 43.070 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.310 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.3150 time to fit residues: 193.7053 Evaluate side-chains 280 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.928 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6846 ------------------------------------------------------------------------------- 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: 10.0000 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 573 HIS D 699 GLN D 840 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1832 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 : 0.652 9.725 23019 Z= 0.339 Chirality : 0.046 0.216 2430 Planarity : 0.006 0.087 2987 Dihedral : 6.014 44.811 2218 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 1.62 % 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: -0.15 (0.28), residues: 317 sheet: -1.58 (0.19), residues: 623 loop : -1.75 (0.17), residues: 1094 *********************** 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 336 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 307 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 21 residues processed: 323 average time/residue: 0.3030 time to fit residues: 144.8155 Evaluate side-chains 294 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 273 time to evaluate : 1.853 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1628 time to fit residues: 9.0092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 153 optimal weight: 0.0870 chunk 125 optimal weight: 0.0010 chunk 50 optimal weight: 0.0040 chunk 184 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 164 optimal weight: 0.1980 chunk 183 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 overall best weight: 0.1776 ------------------------------------------------------------------------------- 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 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 837 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 GLN D 525 HIS D 840 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 16934 Z= 0.152 Angle : 0.602 8.075 23019 Z= 0.307 Chirality : 0.045 0.179 2430 Planarity : 0.005 0.068 2987 Dihedral : 5.519 41.150 2218 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 1.51 % 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: -1.64 (0.18), residues: 2034 helix: 0.61 (0.30), residues: 310 sheet: -1.06 (0.20), residues: 598 loop : -1.61 (0.17), residues: 1126 *********************** 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 337 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 310 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 8 residues processed: 327 average time/residue: 0.3002 time to fit residues: 146.2386 Evaluate side-chains 284 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 276 time to evaluate : 1.973 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2022 time to fit residues: 5.5180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0370 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN A 798 ASN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 840 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 16934 Z= 0.360 Angle : 0.652 10.043 23019 Z= 0.334 Chirality : 0.047 0.303 2430 Planarity : 0.005 0.074 2987 Dihedral : 5.585 38.424 2218 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 2.86 % 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: -1.62 (0.18), residues: 2034 helix: 0.30 (0.30), residues: 318 sheet: -1.08 (0.20), residues: 620 loop : -1.47 (0.18), residues: 1096 *********************** 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 347 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 296 time to evaluate : 1.822 Fit side-chains outliers start: 51 outliers final: 29 residues processed: 324 average time/residue: 0.3191 time to fit residues: 151.5840 Evaluate side-chains 298 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 269 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1612 time to fit residues: 11.4994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 665 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 16934 Z= 0.296 Angle : 0.627 10.770 23019 Z= 0.321 Chirality : 0.046 0.192 2430 Planarity : 0.005 0.059 2987 Dihedral : 5.498 37.510 2218 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 1.79 % 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: -1.54 (0.18), residues: 2034 helix: 0.42 (0.30), residues: 318 sheet: -1.06 (0.20), residues: 614 loop : -1.41 (0.18), residues: 1102 *********************** 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 311 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 279 time to evaluate : 1.889 Fit side-chains outliers start: 32 outliers final: 13 residues processed: 300 average time/residue: 0.3273 time to fit residues: 144.9009 Evaluate side-chains 281 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 268 time to evaluate : 1.921 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1516 time to fit residues: 6.3526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0070 chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 90 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 742 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16934 Z= 0.202 Angle : 0.588 9.281 23019 Z= 0.301 Chirality : 0.044 0.156 2430 Planarity : 0.005 0.069 2987 Dihedral : 5.288 35.187 2218 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 1.46 % 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: 0.67 (0.31), residues: 311 sheet: -0.82 (0.21), residues: 586 loop : -1.36 (0.18), residues: 1137 *********************** 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 322 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 296 time to evaluate : 1.875 Fit side-chains outliers start: 26 outliers final: 9 residues processed: 314 average time/residue: 0.3206 time to fit residues: 148.5288 Evaluate side-chains 280 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 271 time to evaluate : 1.975 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1663 time to fit residues: 5.5581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 111 optimal weight: 10.0000 chunk 143 optimal weight: 0.2980 chunk 165 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 195 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 16934 Z= 0.218 Angle : 0.603 8.897 23019 Z= 0.308 Chirality : 0.045 0.173 2430 Planarity : 0.005 0.068 2987 Dihedral : 5.206 34.143 2218 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 1.29 % 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: -1.23 (0.18), residues: 2034 helix: 0.82 (0.31), residues: 309 sheet: -0.77 (0.21), residues: 596 loop : -1.30 (0.18), residues: 1129 *********************** 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 295 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 272 time to evaluate : 1.977 Fit side-chains outliers start: 23 outliers final: 9 residues processed: 283 average time/residue: 0.3223 time to fit residues: 133.4568 Evaluate side-chains 266 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 257 time to evaluate : 1.899 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1641 time to fit residues: 5.4008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.3980 chunk 116 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 177 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 ASN D 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16934 Z= 0.189 Angle : 0.597 9.117 23019 Z= 0.303 Chirality : 0.044 0.173 2430 Planarity : 0.005 0.057 2987 Dihedral : 5.119 31.748 2218 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 0.84 % 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: -1.11 (0.18), residues: 2034 helix: 0.93 (0.31), residues: 309 sheet: -0.62 (0.22), residues: 575 loop : -1.27 (0.18), residues: 1150 *********************** 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 288 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 273 time to evaluate : 1.965 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 281 average time/residue: 0.3244 time to fit residues: 133.5788 Evaluate side-chains 262 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 256 time to evaluate : 1.898 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1653 time to fit residues: 4.4449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 chunk 182 optimal weight: 0.0980 chunk 109 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 164 optimal weight: 0.0370 chunk 172 optimal weight: 0.8980 chunk 181 optimal weight: 0.5980 chunk 119 optimal weight: 7.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 798 ASN ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 GLN D 837 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16934 Z= 0.172 Angle : 0.589 8.680 23019 Z= 0.299 Chirality : 0.044 0.157 2430 Planarity : 0.005 0.063 2987 Dihedral : 5.039 30.806 2218 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.90 % 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: -1.03 (0.19), residues: 2034 helix: 1.10 (0.31), residues: 303 sheet: -0.61 (0.21), residues: 617 loop : -1.22 (0.18), residues: 1114 *********************** 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 287 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 271 time to evaluate : 1.924 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 277 average time/residue: 0.3179 time to fit residues: 130.3997 Evaluate side-chains 268 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 261 time to evaluate : 1.791 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1604 time to fit residues: 4.5570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 0.2980 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 0.0050 chunk 134 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 161 optimal weight: 0.0020 chunk 16 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 overall best weight: 0.6606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 377 GLN A 798 ASN ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 16934 Z= 0.216 Angle : 0.597 9.424 23019 Z= 0.303 Chirality : 0.044 0.164 2430 Planarity : 0.005 0.064 2987 Dihedral : 5.014 31.257 2218 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.19), residues: 2034 helix: 1.03 (0.31), residues: 305 sheet: -0.57 (0.21), residues: 613 loop : -1.21 (0.18), residues: 1116 ********************** 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 274 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 270 time to evaluate : 1.998 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 272 average time/residue: 0.3229 time to fit residues: 129.1115 Evaluate side-chains 264 residues out of total 1801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1543 time to fit residues: 2.9572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 161 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.0980 chunk 141 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN A 798 ASN ** B 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 GLN D 777 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.181544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132247 restraints weight = 22210.911| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.59 r_work: 0.3257 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16934 Z= 0.181 Angle : 0.596 9.922 23019 Z= 0.301 Chirality : 0.044 0.156 2430 Planarity : 0.005 0.060 2987 Dihedral : 4.948 30.692 2218 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 2034 helix: 1.09 (0.31), residues: 305 sheet: -0.51 (0.21), residues: 600 loop : -1.18 (0.18), residues: 1129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4202.68 seconds wall clock time: 76 minutes 32.96 seconds (4592.96 seconds total)