Starting phenix.real_space_refine on Fri Feb 16 20:43:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn7_22402/02_2024/7jn7_22402_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn7_22402/02_2024/7jn7_22402.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn7_22402/02_2024/7jn7_22402_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn7_22402/02_2024/7jn7_22402_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn7_22402/02_2024/7jn7_22402_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn7_22402/02_2024/7jn7_22402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn7_22402/02_2024/7jn7_22402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn7_22402/02_2024/7jn7_22402_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn7_22402/02_2024/7jn7_22402_updated.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: 5 Type Number sf(0) Gaussians S 64 5.16 5 B 2 2.79 5 C 10586 2.51 5 N 2784 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 TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 486": "OE1" <-> "OE2" 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 PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 720": "OD1" <-> "OD2" Residue "A TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "C TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C ARG 353": "NH1" <-> "NH2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "C ASP 429": "OD1" <-> "OD2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 197": "OD1" <-> "OD2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 477": "OD1" <-> "OD2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D GLU 508": "OE1" <-> "OE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 557": "OD1" <-> "OD2" Residue "D PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 618": "OD1" <-> "OD2" Residue "D TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 678": "OD1" <-> "OD2" Residue "D PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 775": "OE1" <-> "OE2" Residue "D GLU 796": "OE1" <-> "OE2" Residue "D PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 838": "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: 16455 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 6816 Classifications: {'peptide': 846} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 791} 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: 6433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6433 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 52, 'TRANS': 746} Chain breaks: 3 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: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'GK2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'GK2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.03, per 1000 atoms: 0.55 Number of scatterers: 16455 At special positions: 0 Unit cell: (121.986, 128.536, 131.811, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 O 3019 8.00 N 2784 7.00 C 10586 6.00 B 2 5.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.47 Conformation dependent library (CDL) restraints added in 2.6 seconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3826 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 31 sheets defined 15.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 31 through 41 Processing helix chain 'A' and resid 45 through 48 No H-bonds generated for 'chain 'A' and resid 45 through 48' Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 123 through 131 removed outlier: 3.502A pdb=" N ARG A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 342 through 345 No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 446 through 449 No H-bonds generated for 'chain 'A' and resid 446 through 449' Processing helix chain 'A' and resid 662 through 670 Processing helix chain 'A' and resid 687 through 692 removed outlier: 3.781A pdb=" N ALA A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 715 Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 764 through 770 removed outlier: 4.243A pdb=" N ARG A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 770 " --> pdb=" O TYR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 783 Processing helix chain 'A' and resid 786 through 788 No H-bonds generated for 'chain 'A' and resid 786 through 788' Processing helix chain 'A' and resid 790 through 792 No H-bonds generated for 'chain 'A' and resid 790 through 792' Processing helix chain 'A' and resid 813 through 826 Processing helix chain 'A' and resid 845 through 862 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 349 through 361 removed outlier: 4.715A pdb=" N THR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 358 removed outlier: 3.979A pdb=" N VAL C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 41 Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 342 through 345 No H-bonds generated for 'chain 'D' and resid 342 through 345' Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 584 through 586 No H-bonds generated for 'chain 'D' and resid 584 through 586' Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'D' and resid 687 through 693 removed outlier: 3.881A pdb=" N ALA D 692 " --> pdb=" O ARG D 688 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU D 693 " --> pdb=" O PHE D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 715 Processing helix chain 'D' and resid 730 through 742 removed outlier: 4.459A pdb=" N LEU D 735 " --> pdb=" O GLY D 732 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS D 742 " --> pdb=" O GLY D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 761 No H-bonds generated for 'chain 'D' and resid 759 through 761' Processing helix chain 'D' and resid 764 through 770 removed outlier: 3.877A pdb=" N ARG D 769 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR D 770 " --> pdb=" O TYR D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 784 Processing helix chain 'D' and resid 786 through 788 No H-bonds generated for 'chain 'D' and resid 786 through 788' Processing helix chain 'D' and resid 790 through 792 No H-bonds generated for 'chain 'D' and resid 790 through 792' Processing helix chain 'D' and resid 813 through 826 Processing helix chain 'D' and resid 845 through 862 Processing sheet with id= A, first strand: chain 'A' and resid 57 through 60 removed outlier: 6.855A pdb=" N ILE A 91 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ARG A 71 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER A 89 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TYR A 73 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU A 87 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A 75 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N SER A 85 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 142 through 145 removed outlier: 4.638A pdb=" N LEU A 159 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 200 through 205 Processing sheet with id= D, first strand: chain 'A' and resid 237 through 239 removed outlier: 8.951A pdb=" N LEU A 317 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 338 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 256 through 258 Processing sheet with id= F, first strand: chain 'A' and resid 287 through 291 Processing sheet with id= G, first strand: chain 'A' and resid 351 through 357 removed outlier: 6.739A pdb=" N MET A 367 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA A 355 " --> pdb=" O TRP A 365 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP A 365 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP A 357 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR A 363 " --> pdb=" O TRP A 357 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 413 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU A 380 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL A 411 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 439 through 445 removed outlier: 3.659A pdb=" N HIS A 453 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 485 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 505 through 507 Processing sheet with id= J, first strand: chain 'A' and resid 547 through 552 Processing sheet with id= K, first strand: chain 'A' and resid 609 through 614 removed outlier: 4.103A pdb=" N TYR A 622 " --> pdb=" O ASP A 678 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE A 677 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 749 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLY A 728 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 751 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN A 831 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N HIS A 804 " --> pdb=" O GLN A 831 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN A 833 " --> pdb=" O HIS A 804 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 572 through 574 removed outlier: 6.256A pdb=" N VAL A 574 " --> pdb=" O SER A 594 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER A 594 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 234 through 238 removed outlier: 3.936A pdb=" N LEU B 234 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP B 174 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER B 181 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU B 172 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 288 through 292 removed outlier: 6.772A pdb=" N LEU B 200 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE B 248 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY B 198 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 326 through 334 removed outlier: 3.891A pdb=" N LYS B 345 " --> pdb=" O HIS B 326 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 396 through 398 removed outlier: 5.874A pdb=" N TRP B 428 " --> pdb=" O PRO B 434 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 327 through 329 Processing sheet with id= R, first strand: chain 'C' and resid 382 through 386 removed outlier: 3.982A pdb=" N ASP C 436 " --> pdb=" O LEU C 426 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP C 428 " --> pdb=" O PRO C 434 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 57 through 60 removed outlier: 7.289A pdb=" N ILE D 91 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG D 71 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER D 89 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TYR D 73 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU D 87 " --> pdb=" O TYR D 73 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 142 through 145 removed outlier: 4.571A pdb=" N LEU D 159 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 200 through 205 Processing sheet with id= V, first strand: chain 'D' and resid 237 through 239 removed outlier: 9.244A pdb=" N LEU D 317 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU D 338 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 256 through 258 Processing sheet with id= X, first strand: chain 'D' and resid 271 through 273 removed outlier: 3.558A pdb=" N PHE D 322 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 287 through 291 Processing sheet with id= Z, first strand: chain 'D' and resid 351 through 357 removed outlier: 6.743A pdb=" N MET D 367 " --> pdb=" O ALA D 353 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA D 355 " --> pdb=" O TRP D 365 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP D 365 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP D 357 " --> pdb=" O TYR D 363 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR D 363 " --> pdb=" O TRP D 357 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 413 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU D 380 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL D 411 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 440 through 445 removed outlier: 3.543A pdb=" N HIS D 453 " --> pdb=" O ASN D 445 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 505 through 507 Processing sheet with id= AC, first strand: chain 'D' and resid 547 through 552 Processing sheet with id= AD, first strand: chain 'D' and resid 609 through 614 removed outlier: 4.083A pdb=" N TYR D 622 " --> pdb=" O ASP D 678 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE D 677 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL D 749 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N GLY D 728 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE D 751 " --> pdb=" O GLY D 728 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLN D 831 " --> pdb=" O ILE D 802 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N HIS D 804 " --> pdb=" O GLN D 831 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLN D 833 " --> pdb=" O HIS D 804 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 572 through 574 removed outlier: 6.265A pdb=" N VAL D 574 " --> pdb=" O SER D 594 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N SER D 594 " --> pdb=" O VAL D 574 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 6.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2765 1.32 - 1.44: 4784 1.44 - 1.57: 9296 1.57 - 1.69: 4 1.69 - 1.82: 100 Bond restraints: 16949 Sorted by residual: bond pdb=" B15 GK2 A 901 " pdb=" O16 GK2 A 901 " ideal model delta sigma weight residual 1.338 1.535 -0.197 2.00e-02 2.50e+03 9.75e+01 bond pdb=" B15 GK2 D 901 " pdb=" O16 GK2 D 901 " ideal model delta sigma weight residual 1.338 1.533 -0.195 2.00e-02 2.50e+03 9.52e+01 bond pdb=" C2 GK2 D 901 " pdb=" C3 GK2 D 901 " ideal model delta sigma weight residual 1.338 1.516 -0.178 2.00e-02 2.50e+03 7.92e+01 bond pdb=" C2 GK2 A 901 " pdb=" C3 GK2 A 901 " ideal model delta sigma weight residual 1.338 1.515 -0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" B15 GK2 D 901 " pdb=" O17 GK2 D 901 " ideal model delta sigma weight residual 1.364 1.536 -0.172 2.00e-02 2.50e+03 7.42e+01 ... (remaining 16944 not shown) Histogram of bond angle deviations from ideal: 96.19 - 103.98: 351 103.98 - 111.77: 7239 111.77 - 119.56: 6775 119.56 - 127.36: 8403 127.36 - 135.15: 266 Bond angle restraints: 23034 Sorted by residual: angle pdb=" CA PRO D 429 " pdb=" N PRO D 429 " pdb=" CD PRO D 429 " ideal model delta sigma weight residual 112.00 99.80 12.20 1.40e+00 5.10e-01 7.60e+01 angle pdb=" CA GLU D 486 " pdb=" CB GLU D 486 " pdb=" CG GLU D 486 " ideal model delta sigma weight residual 114.10 126.04 -11.94 2.00e+00 2.50e-01 3.57e+01 angle pdb=" C GLU A 321 " pdb=" CA GLU A 321 " pdb=" CB GLU A 321 " ideal model delta sigma weight residual 110.45 100.79 9.66 1.73e+00 3.34e-01 3.12e+01 angle pdb=" C TYR D 428 " pdb=" N PRO D 429 " pdb=" CD PRO D 429 " ideal model delta sigma weight residual 125.00 102.74 22.26 4.10e+00 5.95e-02 2.95e+01 angle pdb=" C SER A 730 " pdb=" CA SER A 730 " pdb=" CB SER A 730 " ideal model delta sigma weight residual 116.63 110.63 6.00 1.16e+00 7.43e-01 2.68e+01 ... (remaining 23029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 8960 18.01 - 36.02: 873 36.02 - 54.03: 139 54.03 - 72.04: 34 72.04 - 90.05: 12 Dihedral angle restraints: 10018 sinusoidal: 4066 harmonic: 5952 Sorted by residual: dihedral pdb=" CA ALA A 155 " pdb=" C ALA A 155 " pdb=" N SER A 156 " pdb=" CA SER A 156 " ideal model delta harmonic sigma weight residual -180.00 -129.78 -50.22 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA MET D 771 " pdb=" C MET D 771 " pdb=" N ASP D 772 " pdb=" CA ASP D 772 " ideal model delta harmonic sigma weight residual -180.00 -131.82 -48.18 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CA SER C 362 " pdb=" C SER C 362 " pdb=" N PRO C 363 " pdb=" CA PRO C 363 " ideal model delta harmonic sigma weight residual -180.00 -141.28 -38.72 0 5.00e+00 4.00e-02 6.00e+01 ... (remaining 10015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1949 0.084 - 0.169: 405 0.169 - 0.253: 64 0.253 - 0.337: 11 0.337 - 0.422: 3 Chirality restraints: 2432 Sorted by residual: chirality pdb=" CG LEU A 664 " pdb=" CB LEU A 664 " pdb=" CD1 LEU A 664 " pdb=" CD2 LEU A 664 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB VAL D 457 " pdb=" CA VAL D 457 " pdb=" CG1 VAL D 457 " pdb=" CG2 VAL D 457 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CB ILE B 347 " pdb=" CA ILE B 347 " pdb=" CG1 ILE B 347 " pdb=" CG2 ILE B 347 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 2429 not shown) Planarity restraints: 2983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 428 " 0.153 5.00e-02 4.00e+02 2.20e-01 7.74e+01 pdb=" N PRO D 429 " -0.379 5.00e-02 4.00e+02 pdb=" CA PRO D 429 " 0.132 5.00e-02 4.00e+02 pdb=" CD PRO D 429 " 0.095 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 808 " -0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" CG ASP D 808 " 0.077 2.00e-02 2.50e+03 pdb=" OD1 ASP D 808 " -0.027 2.00e-02 2.50e+03 pdb=" OD2 ASP D 808 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 768 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C GLU D 768 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU D 768 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG D 769 " -0.023 2.00e-02 2.50e+03 ... (remaining 2980 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 3 2.05 - 2.76: 2419 2.76 - 3.47: 22624 3.47 - 4.19: 42276 4.19 - 4.90: 71724 Nonbonded interactions: 139046 Sorted by model distance: nonbonded pdb=" OG SER A 730 " pdb=" O16 GK2 A 901 " model vdw 1.335 2.440 nonbonded pdb=" OG SER A 730 " pdb=" B15 GK2 A 901 " model vdw 1.434 2.370 nonbonded pdb=" NE ARG A 131 " pdb=" OE1 GLU A 248 " model vdw 1.960 2.520 nonbonded pdb=" O GLY B 259 " pdb=" OH TYR B 322 " model vdw 2.228 2.440 nonbonded pdb=" O ASN D 406 " pdb=" OG SER D 463 " model vdw 2.268 2.440 ... (remaining 139041 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 43 or resid 53 through 76 or resid 86 through 1 \ 09 or resid 139 through 863 or resid 901)) 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: 3.180 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: 13.460 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 46.520 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 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 : 0.009 0.197 16949 Z= 0.600 Angle : 1.286 22.257 23034 Z= 0.697 Chirality : 0.073 0.422 2432 Planarity : 0.010 0.220 2983 Dihedral : 14.775 90.049 6192 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.51 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -3.14 (0.16), residues: 2028 helix: -1.55 (0.24), residues: 294 sheet: -2.16 (0.18), residues: 630 loop : -2.18 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 258 HIS 0.017 0.003 HIS A 68 PHE 0.045 0.004 PHE D 556 TYR 0.058 0.004 TYR A 351 ARG 0.023 0.002 ARG A 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 1.827 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7503 (mp0) REVERT: A 179 GLU cc_start: 0.7309 (tp30) cc_final: 0.6926 (tp30) REVERT: A 575 TYR cc_start: 0.8384 (m-80) cc_final: 0.7782 (m-80) REVERT: A 745 GLN cc_start: 0.7986 (pm20) cc_final: 0.7413 (tp40) REVERT: B 264 SER cc_start: 0.8428 (p) cc_final: 0.8152 (p) REVERT: B 317 SER cc_start: 0.7873 (m) cc_final: 0.7583 (p) REVERT: B 344 THR cc_start: 0.6293 (t) cc_final: 0.5994 (t) REVERT: C 343 LEU cc_start: 0.3916 (mm) cc_final: 0.3710 (mm) REVERT: C 365 MET cc_start: 0.4285 (mmm) cc_final: 0.3927 (mmm) REVERT: D 24 PHE cc_start: 0.6341 (t80) cc_final: 0.5917 (t80) REVERT: D 31 TRP cc_start: 0.5525 (t-100) cc_final: 0.5064 (t-100) REVERT: D 319 LEU cc_start: 0.8140 (mm) cc_final: 0.7804 (mm) REVERT: D 595 MET cc_start: 0.5249 (tpt) cc_final: 0.4624 (tpt) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.2831 time to fit residues: 151.2468 Evaluate side-chains 297 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 68 HIS ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 HIS ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16949 Z= 0.344 Angle : 0.697 8.777 23034 Z= 0.361 Chirality : 0.047 0.179 2432 Planarity : 0.006 0.068 2983 Dihedral : 6.333 48.106 2231 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.62 % Allowed : 10.20 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.17), residues: 2028 helix: -0.18 (0.28), residues: 303 sheet: -1.54 (0.19), residues: 621 loop : -1.92 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 420 HIS 0.013 0.002 HIS A 742 PHE 0.018 0.002 PHE D 689 TYR 0.025 0.002 TYR B 335 ARG 0.006 0.001 ARG A 688 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 329 time to evaluate : 1.798 Fit side-chains revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7529 (tp30) cc_final: 0.7231 (tp30) REVERT: A 575 TYR cc_start: 0.8431 (m-80) cc_final: 0.8044 (m-80) REVERT: C 365 MET cc_start: 0.4356 (mmm) cc_final: 0.3439 (mmm) REVERT: D 24 PHE cc_start: 0.6473 (t80) cc_final: 0.6146 (t80) REVERT: D 31 TRP cc_start: 0.5803 (t-100) cc_final: 0.4988 (t-100) REVERT: D 319 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8174 (mm) REVERT: D 546 PHE cc_start: 0.7887 (m-80) cc_final: 0.7514 (m-80) REVERT: D 587 LYS cc_start: 0.6491 (mtpt) cc_final: 0.6264 (mmtp) REVERT: D 595 MET cc_start: 0.5285 (tpt) cc_final: 0.4966 (tpt) outliers start: 29 outliers final: 15 residues processed: 343 average time/residue: 0.2994 time to fit residues: 154.8785 Evaluate side-chains 299 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 283 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 0.0770 chunk 152 optimal weight: 0.6980 chunk 124 optimal weight: 0.0670 chunk 50 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 163 optimal weight: 0.2980 chunk 182 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 247 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 837 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16949 Z= 0.191 Angle : 0.618 7.250 23034 Z= 0.313 Chirality : 0.045 0.215 2432 Planarity : 0.005 0.056 2983 Dihedral : 5.854 43.639 2231 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.68 % Allowed : 13.84 % Favored : 84.48 % 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: -1.79 (0.17), residues: 2028 helix: 0.34 (0.29), residues: 302 sheet: -1.07 (0.20), residues: 601 loop : -1.70 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 258 HIS 0.014 0.001 HIS D 161 PHE 0.016 0.001 PHE D 556 TYR 0.022 0.002 TYR B 335 ARG 0.007 0.000 ARG D 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 314 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.7253 (m90) cc_final: 0.6986 (m170) REVERT: A 575 TYR cc_start: 0.8405 (m-80) cc_final: 0.8023 (m-80) REVERT: A 667 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8010 (mp) REVERT: A 745 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: B 248 ILE cc_start: 0.8014 (mp) cc_final: 0.7800 (mm) REVERT: C 365 MET cc_start: 0.4194 (mmm) cc_final: 0.3308 (mmm) REVERT: D 24 PHE cc_start: 0.6426 (t80) cc_final: 0.6210 (t80) REVERT: D 31 TRP cc_start: 0.5756 (t-100) cc_final: 0.4987 (t-100) REVERT: D 497 LEU cc_start: 0.7889 (mp) cc_final: 0.7577 (mp) REVERT: D 587 LYS cc_start: 0.6489 (mtpt) cc_final: 0.6213 (mmtp) outliers start: 30 outliers final: 15 residues processed: 331 average time/residue: 0.2859 time to fit residues: 142.8833 Evaluate side-chains 300 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 283 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 184 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 60 GLN A 247 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 16949 Z= 0.556 Angle : 0.766 8.487 23034 Z= 0.395 Chirality : 0.049 0.230 2432 Planarity : 0.006 0.052 2983 Dihedral : 6.339 48.024 2231 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.75 % Allowed : 14.29 % Favored : 81.96 % 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: -2.15 (0.17), residues: 2028 helix: -0.30 (0.28), residues: 302 sheet: -1.35 (0.20), residues: 614 loop : -1.80 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 258 HIS 0.013 0.002 HIS A 804 PHE 0.026 0.003 PHE D 342 TYR 0.026 0.003 TYR B 335 ARG 0.004 0.001 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 306 time to evaluate : 2.015 Fit side-chains REVERT: A 32 ASP cc_start: 0.7698 (t0) cc_final: 0.7494 (t0) REVERT: A 179 GLU cc_start: 0.7544 (tp30) cc_final: 0.6772 (tp30) REVERT: A 369 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8006 (mt) REVERT: A 375 TRP cc_start: 0.7780 (t60) cc_final: 0.7371 (t60) REVERT: A 667 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8117 (mt) REVERT: A 745 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: C 365 MET cc_start: 0.3877 (mmm) cc_final: 0.3002 (mmm) REVERT: D 31 TRP cc_start: 0.6098 (t-100) cc_final: 0.5040 (t-100) REVERT: D 319 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7995 (mm) REVERT: D 587 LYS cc_start: 0.6752 (mtpt) cc_final: 0.6314 (mmtp) REVERT: D 702 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7686 (mm) outliers start: 67 outliers final: 48 residues processed: 338 average time/residue: 0.2926 time to fit residues: 149.4979 Evaluate side-chains 338 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 285 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 625 ILE Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain D residue 683 CYS Chi-restraints excluded: chain D residue 688 ARG Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 854 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 0.7980 chunk 110 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 166 optimal weight: 0.0980 chunk 134 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16949 Z= 0.228 Angle : 0.619 9.223 23034 Z= 0.314 Chirality : 0.045 0.203 2432 Planarity : 0.005 0.049 2983 Dihedral : 5.798 36.828 2231 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.80 % Allowed : 16.92 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -1.71 (0.18), residues: 2028 helix: 0.23 (0.29), residues: 312 sheet: -1.00 (0.20), residues: 622 loop : -1.62 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 258 HIS 0.013 0.001 HIS D 161 PHE 0.017 0.002 PHE D 711 TYR 0.021 0.002 TYR B 335 ARG 0.006 0.000 ARG A 825 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 310 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.7948 (pptt) cc_final: 0.7432 (pttp) REVERT: A 667 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7958 (mp) REVERT: A 745 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: B 248 ILE cc_start: 0.8075 (mp) cc_final: 0.7844 (mm) REVERT: C 365 MET cc_start: 0.3958 (mmm) cc_final: 0.3176 (mmm) REVERT: D 31 TRP cc_start: 0.6073 (t-100) cc_final: 0.4984 (t-100) REVERT: D 319 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7826 (mm) REVERT: D 530 VAL cc_start: 0.8240 (m) cc_final: 0.8036 (t) REVERT: D 587 LYS cc_start: 0.6720 (mtpt) cc_final: 0.6259 (mmtp) outliers start: 50 outliers final: 35 residues processed: 339 average time/residue: 0.2805 time to fit residues: 143.4578 Evaluate side-chains 324 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 286 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 316 THR 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 435 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 625 ILE Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 162 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 247 GLN A 418 ASN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16949 Z= 0.247 Angle : 0.606 7.777 23034 Z= 0.307 Chirality : 0.045 0.181 2432 Planarity : 0.005 0.047 2983 Dihedral : 5.632 36.195 2231 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.42 % Allowed : 17.54 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -1.56 (0.18), residues: 2028 helix: 0.40 (0.29), residues: 312 sheet: -0.90 (0.21), residues: 621 loop : -1.54 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 258 HIS 0.012 0.001 HIS D 161 PHE 0.016 0.002 PHE A 747 TYR 0.031 0.002 TYR B 323 ARG 0.004 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 308 time to evaluate : 1.908 Fit side-chains REVERT: A 179 GLU cc_start: 0.7538 (tp30) cc_final: 0.6961 (tp30) REVERT: A 279 GLU cc_start: 0.7235 (tt0) cc_final: 0.6949 (tt0) REVERT: A 369 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8041 (mt) REVERT: A 462 LYS cc_start: 0.7912 (pptt) cc_final: 0.7403 (pttp) REVERT: A 667 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8014 (mp) REVERT: A 771 MET cc_start: 0.8271 (mmm) cc_final: 0.8048 (mtp) REVERT: C 365 MET cc_start: 0.3977 (mmm) cc_final: 0.3176 (mmm) REVERT: D 31 TRP cc_start: 0.6172 (t-100) cc_final: 0.5025 (t-100) REVERT: D 319 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7777 (mm) REVERT: D 485 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6474 (pm20) REVERT: D 587 LYS cc_start: 0.6725 (mtpt) cc_final: 0.6274 (mmtp) outliers start: 61 outliers final: 48 residues processed: 347 average time/residue: 0.2792 time to fit residues: 146.1002 Evaluate side-chains 338 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 286 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 316 THR 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 435 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 625 ILE Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 142 optimal weight: 0.1980 chunk 110 optimal weight: 20.0000 chunk 164 optimal weight: 0.3980 chunk 109 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 247 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16949 Z= 0.296 Angle : 0.628 7.996 23034 Z= 0.318 Chirality : 0.046 0.231 2432 Planarity : 0.005 0.046 2983 Dihedral : 5.651 36.512 2231 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.81 % Allowed : 17.70 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -1.51 (0.18), residues: 2028 helix: 0.44 (0.29), residues: 311 sheet: -0.79 (0.21), residues: 615 loop : -1.56 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 258 HIS 0.010 0.001 HIS D 161 PHE 0.017 0.002 PHE A 747 TYR 0.027 0.002 TYR B 323 ARG 0.008 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 294 time to evaluate : 1.940 Fit side-chains REVERT: A 279 GLU cc_start: 0.7265 (tt0) cc_final: 0.6982 (tt0) REVERT: A 369 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8015 (mt) REVERT: A 462 LYS cc_start: 0.7960 (pptt) cc_final: 0.7419 (pttp) REVERT: A 667 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8007 (mp) REVERT: A 763 ASP cc_start: 0.8344 (p0) cc_final: 0.8097 (p0) REVERT: C 365 MET cc_start: 0.4021 (mmm) cc_final: 0.3227 (mmm) REVERT: D 31 TRP cc_start: 0.6250 (t-100) cc_final: 0.5129 (t-100) REVERT: D 218 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7761 (pt0) REVERT: D 587 LYS cc_start: 0.6742 (mtpt) cc_final: 0.6327 (mmtp) REVERT: D 702 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7614 (mm) outliers start: 68 outliers final: 54 residues processed: 335 average time/residue: 0.2837 time to fit residues: 143.3794 Evaluate side-chains 342 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 284 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 316 THR 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 383 LYS Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 625 ILE Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 676 VAL Chi-restraints excluded: chain D residue 702 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 0.0070 chunk 77 optimal weight: 0.0870 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 96 optimal weight: 0.0370 chunk 18 optimal weight: 0.4980 chunk 153 optimal weight: 1.9990 overall best weight: 0.1372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 516 GLN A 812 HIS B 224 HIS ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN D 373 GLN ** D 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16949 Z= 0.162 Angle : 0.585 8.743 23034 Z= 0.294 Chirality : 0.044 0.167 2432 Planarity : 0.004 0.044 2983 Dihedral : 5.297 35.377 2231 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.86 % Allowed : 18.82 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.00 % 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: -1.32 (0.18), residues: 2028 helix: 0.76 (0.29), residues: 307 sheet: -0.72 (0.21), residues: 629 loop : -1.45 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 258 HIS 0.009 0.001 HIS D 161 PHE 0.012 0.001 PHE D 711 TYR 0.028 0.001 TYR B 323 ARG 0.012 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 314 time to evaluate : 1.812 Fit side-chains REVERT: A 179 GLU cc_start: 0.7551 (tp30) cc_final: 0.6987 (tp30) REVERT: A 421 ILE cc_start: 0.8140 (mm) cc_final: 0.7916 (mm) REVERT: A 462 LYS cc_start: 0.7831 (pptt) cc_final: 0.7222 (pttp) REVERT: A 667 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7942 (mp) REVERT: A 843 ARG cc_start: 0.7447 (mtt-85) cc_final: 0.6547 (ttm-80) REVERT: C 365 MET cc_start: 0.4233 (mmm) cc_final: 0.3459 (mmm) REVERT: D 31 TRP cc_start: 0.6020 (t-100) cc_final: 0.4932 (t-100) REVERT: D 485 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6354 (pm20) REVERT: D 587 LYS cc_start: 0.6774 (mtpt) cc_final: 0.6315 (mmtp) REVERT: D 595 MET cc_start: 0.6013 (tpt) cc_final: 0.5454 (tpt) REVERT: D 648 GLN cc_start: 0.8408 (mp10) cc_final: 0.7873 (mp10) outliers start: 51 outliers final: 30 residues processed: 346 average time/residue: 0.2811 time to fit residues: 147.3009 Evaluate side-chains 318 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 286 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 676 VAL Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 0.0670 chunk 186 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 181 optimal weight: 0.0470 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 163 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 247 GLN A 340 GLN A 516 GLN ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN D 516 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 ASN ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 GLN ** D 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16949 Z= 0.191 Angle : 0.594 10.458 23034 Z= 0.299 Chirality : 0.045 0.389 2432 Planarity : 0.005 0.045 2983 Dihedral : 5.258 35.763 2231 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.80 % Allowed : 19.33 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.00 % 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: -1.21 (0.18), residues: 2028 helix: 0.87 (0.30), residues: 306 sheet: -0.62 (0.21), residues: 628 loop : -1.41 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 258 HIS 0.010 0.001 HIS D 161 PHE 0.012 0.001 PHE D 711 TYR 0.027 0.002 TYR B 323 ARG 0.011 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 287 time to evaluate : 1.952 Fit side-chains REVERT: A 179 GLU cc_start: 0.7530 (tp30) cc_final: 0.6808 (tp30) REVERT: A 462 LYS cc_start: 0.7848 (pptt) cc_final: 0.7517 (pttt) REVERT: A 667 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8032 (mt) REVERT: A 843 ARG cc_start: 0.7454 (mtt-85) cc_final: 0.6578 (ttm-80) REVERT: C 365 MET cc_start: 0.4217 (mmm) cc_final: 0.3454 (mmm) REVERT: D 31 TRP cc_start: 0.6090 (t-100) cc_final: 0.5015 (t-100) REVERT: D 595 MET cc_start: 0.6000 (tpt) cc_final: 0.5460 (tpt) REVERT: D 648 GLN cc_start: 0.8447 (mp10) cc_final: 0.7905 (mp10) REVERT: D 693 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8187 (pp) REVERT: D 703 GLU cc_start: 0.7595 (mp0) cc_final: 0.7301 (mp0) outliers start: 50 outliers final: 36 residues processed: 316 average time/residue: 0.2822 time to fit residues: 135.3335 Evaluate side-chains 314 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 276 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 373 GLN Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 516 GLN Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 676 VAL Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 133 optimal weight: 0.0870 chunk 201 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 516 GLN ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN D 516 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 GLN ** D 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16949 Z= 0.330 Angle : 0.653 12.099 23034 Z= 0.330 Chirality : 0.047 0.539 2432 Planarity : 0.005 0.044 2983 Dihedral : 5.448 36.665 2231 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.69 % Allowed : 19.72 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.37 (0.18), residues: 2028 helix: 0.64 (0.29), residues: 305 sheet: -0.69 (0.21), residues: 621 loop : -1.49 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 428 HIS 0.011 0.001 HIS D 161 PHE 0.014 0.002 PHE A 559 TYR 0.038 0.002 TYR B 323 ARG 0.011 0.001 ARG A 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 293 time to evaluate : 2.038 Fit side-chains REVERT: A 229 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5606 (pp) REVERT: A 279 GLU cc_start: 0.7224 (tt0) cc_final: 0.6947 (tt0) REVERT: A 462 LYS cc_start: 0.7893 (pptt) cc_final: 0.7575 (pttt) REVERT: A 667 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8071 (mt) REVERT: C 365 MET cc_start: 0.4256 (mmm) cc_final: 0.3471 (mmm) REVERT: D 31 TRP cc_start: 0.6265 (t-100) cc_final: 0.5148 (t-100) REVERT: D 595 MET cc_start: 0.6073 (tpt) cc_final: 0.5489 (tpt) REVERT: D 693 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8274 (pp) REVERT: D 735 LEU cc_start: 0.8520 (mt) cc_final: 0.8173 (mt) outliers start: 48 outliers final: 40 residues processed: 321 average time/residue: 0.2865 time to fit residues: 140.1626 Evaluate side-chains 327 residues out of total 1799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 284 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 413 TYR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 745 GLN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 487 ILE Chi-restraints excluded: chain D residue 516 GLN Chi-restraints excluded: chain D residue 625 ILE Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 676 VAL Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 790 VAL Chi-restraints excluded: chain D residue 811 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 516 GLN ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.192036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147834 restraints weight = 21391.596| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.70 r_work: 0.3593 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16949 Z= 0.282 Angle : 0.640 11.081 23034 Z= 0.322 Chirality : 0.047 0.501 2432 Planarity : 0.005 0.043 2983 Dihedral : 5.469 36.659 2231 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.91 % Allowed : 19.83 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.35 (0.18), residues: 2028 helix: 0.68 (0.29), residues: 303 sheet: -0.69 (0.21), residues: 624 loop : -1.48 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 428 HIS 0.011 0.001 HIS D 161 PHE 0.013 0.002 PHE A 253 TYR 0.034 0.002 TYR B 323 ARG 0.010 0.001 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4511.84 seconds wall clock time: 82 minutes 30.69 seconds (4950.69 seconds total)