Starting phenix.real_space_refine on Thu Mar 21 12:52:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdc_15981/03_2024/8bdc_15981.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdc_15981/03_2024/8bdc_15981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdc_15981/03_2024/8bdc_15981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdc_15981/03_2024/8bdc_15981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdc_15981/03_2024/8bdc_15981.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdc_15981/03_2024/8bdc_15981.pdb" } resolution = 2.65 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= 0.007 sd= 0.075 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 136 5.16 5 Na 8 4.78 5 C 19852 2.51 5 N 4928 2.21 5 O 5204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30132 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7412 Classifications: {'peptide': 963} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 938} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 583 Unresolved non-hydrogen dihedrals: 396 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 26, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 295 Chain: "B" Number of atoms: 7412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7412 Classifications: {'peptide': 963} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 938} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 583 Unresolved non-hydrogen dihedrals: 396 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 26, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 295 Chain: "C" Number of atoms: 7412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7412 Classifications: {'peptide': 963} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 938} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 583 Unresolved non-hydrogen dihedrals: 396 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 26, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 295 Chain: "D" Number of atoms: 7412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7412 Classifications: {'peptide': 963} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 938} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 480 Unresolved non-hydrogen angles: 583 Unresolved non-hydrogen dihedrals: 396 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 26, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 295 Chain: "A" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 121 Unusual residues: {' NA': 2, 'POV': 1, 'UND': 1, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 121 Unusual residues: {' NA': 2, 'POV': 1, 'UND': 1, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 121 Unusual residues: {' NA': 2, 'POV': 1, 'UND': 1, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 121 Unusual residues: {' NA': 2, 'POV': 1, 'UND': 1, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 16.01, per 1000 atoms: 0.53 Number of scatterers: 30132 At special positions: 0 Unit cell: (159.9, 159.9, 145.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 4 15.00 Na 8 11.00 O 5204 8.00 N 4928 7.00 C 19852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 68 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 68 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 68 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 68 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.76 Conformation dependent library (CDL) restraints added in 5.6 seconds 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7328 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 12 sheets defined 69.5% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.652A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 203 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.518A pdb=" N ASP A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 removed outlier: 3.547A pdb=" N VAL A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.879A pdb=" N CYS A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 418 Processing helix chain 'A' and resid 419 through 424 removed outlier: 3.640A pdb=" N LYS A 423 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 454 through 457 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 533 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.757A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 607 through 636 Processing helix chain 'A' and resid 637 through 645 Processing helix chain 'A' and resid 648 through 652 removed outlier: 3.815A pdb=" N TRP A 651 " --> pdb=" O CYS A 648 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 652 " --> pdb=" O GLU A 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 648 through 652' Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'A' and resid 702 through 708 removed outlier: 3.776A pdb=" N GLY A 708 " --> pdb=" O VAL A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 732 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 791 through 794 removed outlier: 3.574A pdb=" N PHE A 794 " --> pdb=" O VAL A 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 791 through 794' Processing helix chain 'A' and resid 798 through 818 removed outlier: 3.638A pdb=" N HIS A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 852 Processing helix chain 'A' and resid 856 through 889 removed outlier: 3.532A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 912 Proline residue: A 907 - end of helix Processing helix chain 'A' and resid 955 through 980 Processing helix chain 'A' and resid 981 through 983 No H-bonds generated for 'chain 'A' and resid 981 through 983' Processing helix chain 'A' and resid 991 through 1007 Processing helix chain 'A' and resid 1015 through 1030 removed outlier: 3.951A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1072 Processing helix chain 'A' and resid 1078 through 1104 Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.651A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 203 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.518A pdb=" N ASP B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.547A pdb=" N VAL B 354 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.879A pdb=" N CYS B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 418 Processing helix chain 'B' and resid 419 through 424 removed outlier: 3.639A pdb=" N LYS B 423 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 454 through 457 Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 533 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.757A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 586 through 602 Processing helix chain 'B' and resid 607 through 636 Processing helix chain 'B' and resid 637 through 645 Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.815A pdb=" N TRP B 651 " --> pdb=" O CYS B 648 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 652 " --> pdb=" O GLU B 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 648 through 652' Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 Processing helix chain 'B' and resid 702 through 708 removed outlier: 3.776A pdb=" N GLY B 708 " --> pdb=" O VAL B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 732 Processing helix chain 'B' and resid 733 through 759 Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 791 through 794 removed outlier: 3.574A pdb=" N PHE B 794 " --> pdb=" O VAL B 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 791 through 794' Processing helix chain 'B' and resid 798 through 818 removed outlier: 3.638A pdb=" N HIS B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 852 Processing helix chain 'B' and resid 856 through 889 removed outlier: 3.531A pdb=" N ILE B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 912 Proline residue: B 907 - end of helix Processing helix chain 'B' and resid 955 through 980 Processing helix chain 'B' and resid 981 through 983 No H-bonds generated for 'chain 'B' and resid 981 through 983' Processing helix chain 'B' and resid 991 through 1007 Processing helix chain 'B' and resid 1015 through 1030 removed outlier: 3.951A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1072 Processing helix chain 'B' and resid 1078 through 1104 Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.652A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 203 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.518A pdb=" N ASP C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 338 " --> pdb=" O GLN C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 362 removed outlier: 3.548A pdb=" N VAL C 354 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.879A pdb=" N CYS C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 418 Processing helix chain 'C' and resid 419 through 424 removed outlier: 3.640A pdb=" N LYS C 423 " --> pdb=" O GLU C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 533 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.757A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 582 Processing helix chain 'C' and resid 586 through 602 Processing helix chain 'C' and resid 607 through 636 Processing helix chain 'C' and resid 637 through 645 Processing helix chain 'C' and resid 648 through 652 removed outlier: 3.814A pdb=" N TRP C 651 " --> pdb=" O CYS C 648 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY C 652 " --> pdb=" O GLU C 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 648 through 652' Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 Processing helix chain 'C' and resid 702 through 708 removed outlier: 3.776A pdb=" N GLY C 708 " --> pdb=" O VAL C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 732 Processing helix chain 'C' and resid 733 through 759 Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 791 through 794 removed outlier: 3.574A pdb=" N PHE C 794 " --> pdb=" O VAL C 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 791 through 794' Processing helix chain 'C' and resid 798 through 818 removed outlier: 3.638A pdb=" N HIS C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 852 Processing helix chain 'C' and resid 856 through 889 removed outlier: 3.530A pdb=" N ILE C 865 " --> pdb=" O GLN C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 912 Proline residue: C 907 - end of helix Processing helix chain 'C' and resid 955 through 980 Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 991 through 1007 Processing helix chain 'C' and resid 1015 through 1030 removed outlier: 3.951A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1072 Processing helix chain 'C' and resid 1078 through 1104 Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.650A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 203 Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.518A pdb=" N ASP D 337 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 338 " --> pdb=" O GLN D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 362 removed outlier: 3.548A pdb=" N VAL D 354 " --> pdb=" O THR D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'D' and resid 370 through 387 removed outlier: 3.878A pdb=" N CYS D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 418 Processing helix chain 'D' and resid 419 through 424 removed outlier: 3.640A pdb=" N LYS D 423 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 533 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.757A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 582 Processing helix chain 'D' and resid 586 through 602 Processing helix chain 'D' and resid 607 through 636 Processing helix chain 'D' and resid 637 through 645 Processing helix chain 'D' and resid 648 through 652 removed outlier: 3.815A pdb=" N TRP D 651 " --> pdb=" O CYS D 648 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY D 652 " --> pdb=" O GLU D 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 648 through 652' Processing helix chain 'D' and resid 655 through 663 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 Processing helix chain 'D' and resid 702 through 708 removed outlier: 3.775A pdb=" N GLY D 708 " --> pdb=" O VAL D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 733 through 759 Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 791 through 794 removed outlier: 3.575A pdb=" N PHE D 794 " --> pdb=" O VAL D 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 791 through 794' Processing helix chain 'D' and resid 798 through 818 removed outlier: 3.638A pdb=" N HIS D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 852 Processing helix chain 'D' and resid 856 through 889 removed outlier: 3.532A pdb=" N ILE D 865 " --> pdb=" O GLN D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 912 Proline residue: D 907 - end of helix Processing helix chain 'D' and resid 955 through 980 Processing helix chain 'D' and resid 981 through 983 No H-bonds generated for 'chain 'D' and resid 981 through 983' Processing helix chain 'D' and resid 991 through 1007 Processing helix chain 'D' and resid 1015 through 1030 removed outlier: 3.951A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1072 Processing helix chain 'D' and resid 1078 through 1104 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 removed outlier: 3.650A pdb=" N LYS A 96 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 239 removed outlier: 6.763A pdb=" N LYS A 116 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU A 262 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 118 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 264 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A 120 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE A 179 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE A 214 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR A 181 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ALA A 216 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 146 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A 306 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL A 327 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL A 329 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ALA A 305 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 54 removed outlier: 3.649A pdb=" N LYS B 96 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AA6, first strand: chain 'B' and resid 237 through 239 removed outlier: 6.763A pdb=" N LYS B 116 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 262 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 118 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP B 264 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU B 120 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE B 179 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE B 214 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR B 181 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ALA B 216 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 146 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN B 306 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL B 327 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL B 329 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ALA B 305 " --> pdb=" O VAL B 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 54 removed outlier: 3.650A pdb=" N LYS C 96 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA9, first strand: chain 'C' and resid 237 through 239 removed outlier: 6.762A pdb=" N LYS C 116 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU C 262 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE C 118 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP C 264 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU C 120 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE C 179 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE C 214 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR C 181 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ALA C 216 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 146 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C 306 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL C 327 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL C 329 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA C 305 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 50 through 54 removed outlier: 3.649A pdb=" N LYS D 96 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 56 through 57 Processing sheet with id=AB3, first strand: chain 'D' and resid 237 through 239 removed outlier: 6.762A pdb=" N LYS D 116 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU D 262 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE D 118 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP D 264 " --> pdb=" O ILE D 118 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU D 120 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE D 179 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE D 214 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR D 181 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ALA D 216 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE D 146 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN D 306 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL D 327 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL D 329 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ALA D 305 " --> pdb=" O VAL D 329 " (cutoff:3.500A) 1965 hydrogen bonds defined for protein. 5811 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: 11.32 Time building geometry restraints manager: 12.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5111 1.33 - 1.45: 8429 1.45 - 1.58: 17108 1.58 - 1.70: 8 1.70 - 1.83: 200 Bond restraints: 30856 Sorted by residual: bond pdb=" CAX Y01 C1203 " pdb=" OAH Y01 C1203 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" CAX Y01 A1201 " pdb=" OAH Y01 A1201 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" CAX Y01 B1201 " pdb=" OAH Y01 B1201 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" CAX Y01 B1203 " pdb=" OAH Y01 B1203 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" CAX Y01 C1201 " pdb=" OAH Y01 C1201 " ideal model delta sigma weight residual 1.248 1.308 -0.060 2.00e-02 2.50e+03 8.93e+00 ... (remaining 30851 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.11: 371 105.11 - 112.34: 16046 112.34 - 119.58: 9553 119.58 - 126.81: 15582 126.81 - 134.05: 464 Bond angle restraints: 42016 Sorted by residual: angle pdb=" N THR A 795 " pdb=" CA THR A 795 " pdb=" C THR A 795 " ideal model delta sigma weight residual 114.56 110.70 3.86 1.27e+00 6.20e-01 9.23e+00 angle pdb=" N THR D 795 " pdb=" CA THR D 795 " pdb=" C THR D 795 " ideal model delta sigma weight residual 114.56 110.72 3.84 1.27e+00 6.20e-01 9.15e+00 angle pdb=" N THR C 795 " pdb=" CA THR C 795 " pdb=" C THR C 795 " ideal model delta sigma weight residual 114.56 110.75 3.81 1.27e+00 6.20e-01 9.01e+00 angle pdb=" N THR B 795 " pdb=" CA THR B 795 " pdb=" C THR B 795 " ideal model delta sigma weight residual 114.56 110.76 3.80 1.27e+00 6.20e-01 8.96e+00 angle pdb=" CA THR B 795 " pdb=" C THR B 795 " pdb=" N ASP B 796 " ideal model delta sigma weight residual 119.26 116.93 2.33 1.14e+00 7.69e-01 4.17e+00 ... (remaining 42011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15982 17.97 - 35.93: 1627 35.93 - 53.90: 526 53.90 - 71.87: 97 71.87 - 89.84: 36 Dihedral angle restraints: 18268 sinusoidal: 6972 harmonic: 11296 Sorted by residual: dihedral pdb=" CG ARG B 784 " pdb=" CD ARG B 784 " pdb=" NE ARG B 784 " pdb=" CZ ARG B 784 " ideal model delta sinusoidal sigma weight residual -90.00 -134.98 44.98 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG C 784 " pdb=" CD ARG C 784 " pdb=" NE ARG C 784 " pdb=" CZ ARG C 784 " ideal model delta sinusoidal sigma weight residual -90.00 -134.97 44.97 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG A 784 " pdb=" CD ARG A 784 " pdb=" NE ARG A 784 " pdb=" CZ ARG A 784 " ideal model delta sinusoidal sigma weight residual -90.00 -134.96 44.96 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 18265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3173 0.028 - 0.056: 1022 0.056 - 0.083: 463 0.083 - 0.111: 179 0.111 - 0.139: 19 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CA ILE A1011 " pdb=" N ILE A1011 " pdb=" C ILE A1011 " pdb=" CB ILE A1011 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE B1011 " pdb=" N ILE B1011 " pdb=" C ILE B1011 " pdb=" CB ILE B1011 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE C1011 " pdb=" N ILE C1011 " pdb=" C ILE C1011 " pdb=" CB ILE C1011 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 4853 not shown) Planarity restraints: 5164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 763 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO B 764 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 763 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO D 764 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 764 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 764 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 763 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 764 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 764 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 764 " -0.021 5.00e-02 4.00e+02 ... (remaining 5161 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 8346 2.81 - 3.33: 29305 3.33 - 3.85: 52609 3.85 - 4.38: 58914 4.38 - 4.90: 103004 Nonbonded interactions: 252178 Sorted by model distance: nonbonded pdb=" OH TYR A 117 " pdb=" O LEU A 226 " model vdw 2.285 2.440 nonbonded pdb=" OH TYR D 117 " pdb=" O LEU D 226 " model vdw 2.285 2.440 nonbonded pdb=" OH TYR B 117 " pdb=" O LEU B 226 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR C 117 " pdb=" O LEU C 226 " model vdw 2.286 2.440 nonbonded pdb=" O VAL C 728 " pdb=" OG1 THR C 732 " model vdw 2.296 2.440 ... (remaining 252173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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=1.00 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: 5.740 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: 16.810 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 78.290 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.003 0.060 30856 Z= 0.187 Angle : 0.410 7.095 42016 Z= 0.213 Chirality : 0.036 0.139 4856 Planarity : 0.003 0.038 5164 Dihedral : 16.761 89.835 10928 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.15 % Allowed : 22.54 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.17 (0.14), residues: 3780 helix: 2.37 (0.10), residues: 2520 sheet: -1.23 (0.36), residues: 212 loop : -0.28 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 877 HIS 0.002 0.000 HIS A 500 PHE 0.013 0.001 PHE A 165 TYR 0.015 0.001 TYR D 621 ARG 0.001 0.000 ARG A 998 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 607 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7559 (mt-10) REVERT: A 219 MET cc_start: 0.8308 (mmm) cc_final: 0.8055 (mmt) REVERT: A 396 MET cc_start: 0.7663 (mtm) cc_final: 0.7124 (mtp) REVERT: A 462 MET cc_start: 0.8876 (tpt) cc_final: 0.8561 (tpt) REVERT: A 655 ASN cc_start: 0.8165 (t0) cc_final: 0.7714 (t0) REVERT: B 98 PHE cc_start: 0.7479 (m-80) cc_final: 0.7277 (m-80) REVERT: B 101 ASP cc_start: 0.7887 (p0) cc_final: 0.7595 (p0) REVERT: B 194 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 219 MET cc_start: 0.8282 (mmm) cc_final: 0.8015 (mmt) REVERT: B 396 MET cc_start: 0.7660 (mtm) cc_final: 0.7136 (mtp) REVERT: B 655 ASN cc_start: 0.8182 (t0) cc_final: 0.7704 (t0) REVERT: C 98 PHE cc_start: 0.7421 (m-80) cc_final: 0.7213 (m-80) REVERT: C 101 ASP cc_start: 0.7913 (p0) cc_final: 0.7628 (p0) REVERT: C 194 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7565 (mt-10) REVERT: C 219 MET cc_start: 0.8281 (mmm) cc_final: 0.8022 (mmt) REVERT: C 396 MET cc_start: 0.7677 (mtm) cc_final: 0.7109 (mtp) REVERT: C 462 MET cc_start: 0.8872 (tpt) cc_final: 0.8553 (tpt) REVERT: C 655 ASN cc_start: 0.8112 (t0) cc_final: 0.7613 (t0) REVERT: D 194 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7533 (mt-10) REVERT: D 219 MET cc_start: 0.8300 (mmm) cc_final: 0.8048 (mmt) REVERT: D 396 MET cc_start: 0.7674 (mtm) cc_final: 0.7131 (mtp) REVERT: D 462 MET cc_start: 0.8879 (tpt) cc_final: 0.8631 (tpt) REVERT: D 655 ASN cc_start: 0.8090 (t0) cc_final: 0.7625 (t0) outliers start: 63 outliers final: 52 residues processed: 662 average time/residue: 1.1963 time to fit residues: 949.7956 Evaluate side-chains 547 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 495 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 898 TRP Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 898 TRP Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 903 VAL Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.5980 chunk 291 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 348 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 294 ASN A 437 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN B 294 ASN B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN D 671 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 30856 Z= 0.323 Angle : 0.523 6.892 42016 Z= 0.272 Chirality : 0.041 0.142 4856 Planarity : 0.004 0.055 5164 Dihedral : 8.065 79.793 4894 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.85 % Allowed : 22.81 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.81 (0.14), residues: 3780 helix: 2.10 (0.10), residues: 2552 sheet: -1.57 (0.34), residues: 220 loop : -0.45 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 426 HIS 0.004 0.001 HIS B 667 PHE 0.018 0.002 PHE D 629 TYR 0.021 0.002 TYR C 621 ARG 0.004 0.000 ARG C 713 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 507 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8403 (tp) REVERT: A 219 MET cc_start: 0.8300 (mmm) cc_final: 0.8044 (mmt) REVERT: A 378 ILE cc_start: 0.8334 (mm) cc_final: 0.7907 (mt) REVERT: A 655 ASN cc_start: 0.8586 (t0) cc_final: 0.8020 (t0) REVERT: A 851 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7403 (tpt-90) REVERT: B 98 PHE cc_start: 0.7736 (m-80) cc_final: 0.7489 (m-80) REVERT: B 219 MET cc_start: 0.8293 (mmm) cc_final: 0.8046 (mmt) REVERT: B 378 ILE cc_start: 0.8272 (mm) cc_final: 0.7861 (mt) REVERT: B 655 ASN cc_start: 0.8588 (t0) cc_final: 0.8042 (t0) REVERT: B 851 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.7320 (tpt-90) REVERT: B 1009 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8133 (mp) REVERT: C 132 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8407 (tp) REVERT: C 219 MET cc_start: 0.8284 (mmm) cc_final: 0.8029 (mmt) REVERT: C 378 ILE cc_start: 0.8293 (mm) cc_final: 0.7866 (mt) REVERT: C 655 ASN cc_start: 0.8568 (t0) cc_final: 0.8029 (t0) REVERT: C 851 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.7339 (tpt-90) REVERT: D 219 MET cc_start: 0.8314 (mmm) cc_final: 0.8059 (mmt) REVERT: D 378 ILE cc_start: 0.8345 (mm) cc_final: 0.7931 (mt) REVERT: D 655 ASN cc_start: 0.8562 (t0) cc_final: 0.7991 (t0) REVERT: D 851 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7296 (tpt-90) outliers start: 171 outliers final: 61 residues processed: 611 average time/residue: 1.2166 time to fit residues: 889.3778 Evaluate side-chains 553 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 485 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1024 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 290 optimal weight: 8.9990 chunk 237 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 349 optimal weight: 0.8980 chunk 377 optimal weight: 0.8980 chunk 311 optimal weight: 0.9990 chunk 346 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 280 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30856 Z= 0.209 Angle : 0.463 6.252 42016 Z= 0.243 Chirality : 0.038 0.138 4856 Planarity : 0.004 0.049 5164 Dihedral : 7.453 78.562 4852 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 5.95 % Allowed : 24.11 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.89 (0.14), residues: 3780 helix: 2.22 (0.10), residues: 2548 sheet: -1.65 (0.34), residues: 220 loop : -0.57 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 426 HIS 0.003 0.001 HIS C 667 PHE 0.021 0.001 PHE C 44 TYR 0.017 0.001 TYR D 621 ARG 0.004 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 504 time to evaluate : 3.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.7913 (tp30) cc_final: 0.7535 (tp30) REVERT: A 161 MET cc_start: 0.8215 (tpp) cc_final: 0.7619 (mmm) REVERT: A 219 MET cc_start: 0.8283 (mmm) cc_final: 0.8023 (mmt) REVERT: A 378 ILE cc_start: 0.8298 (mm) cc_final: 0.7869 (mt) REVERT: A 482 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7432 (tp) REVERT: A 655 ASN cc_start: 0.8387 (t0) cc_final: 0.7951 (t0) REVERT: A 851 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.6963 (tpt-90) REVERT: A 900 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: A 1009 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8144 (mp) REVERT: B 131 GLU cc_start: 0.7918 (tp30) cc_final: 0.6885 (tp30) REVERT: B 132 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8351 (tp) REVERT: B 161 MET cc_start: 0.8204 (tpp) cc_final: 0.7613 (mmm) REVERT: B 219 MET cc_start: 0.8290 (mmm) cc_final: 0.8049 (mmt) REVERT: B 378 ILE cc_start: 0.8266 (mm) cc_final: 0.7841 (mt) REVERT: B 482 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7433 (tp) REVERT: B 655 ASN cc_start: 0.8396 (t0) cc_final: 0.7949 (t0) REVERT: B 759 ASP cc_start: 0.7353 (t70) cc_final: 0.7112 (t0) REVERT: B 851 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.6961 (tpt-90) REVERT: B 900 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: C 131 GLU cc_start: 0.7918 (tp30) cc_final: 0.7538 (tp30) REVERT: C 161 MET cc_start: 0.8197 (tpp) cc_final: 0.7607 (mmm) REVERT: C 219 MET cc_start: 0.8281 (mmm) cc_final: 0.8008 (mmt) REVERT: C 228 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7302 (mmm-85) REVERT: C 482 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7449 (tp) REVERT: C 655 ASN cc_start: 0.8382 (t0) cc_final: 0.7926 (t0) REVERT: C 851 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.6970 (tpt-90) REVERT: C 900 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: D 131 GLU cc_start: 0.7926 (tp30) cc_final: 0.5955 (tp30) REVERT: D 132 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8374 (tp) REVERT: D 161 MET cc_start: 0.8218 (tpp) cc_final: 0.7613 (mmm) REVERT: D 219 MET cc_start: 0.8276 (mmm) cc_final: 0.8017 (mmt) REVERT: D 228 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7308 (mmm-85) REVERT: D 458 LEU cc_start: 0.7651 (pp) cc_final: 0.7450 (pp) REVERT: D 482 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7426 (tp) REVERT: D 655 ASN cc_start: 0.8374 (t0) cc_final: 0.7914 (t0) REVERT: D 851 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.6966 (tpt-90) outliers start: 174 outliers final: 77 residues processed: 621 average time/residue: 1.1823 time to fit residues: 885.1189 Evaluate side-chains 572 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 479 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 900 PHE Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 900 PHE Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 900 PHE Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1024 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 0.5980 chunk 350 optimal weight: 0.8980 chunk 371 optimal weight: 6.9990 chunk 183 optimal weight: 0.5980 chunk 332 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30856 Z= 0.178 Angle : 0.447 7.798 42016 Z= 0.234 Chirality : 0.037 0.138 4856 Planarity : 0.004 0.048 5164 Dihedral : 7.306 77.560 4852 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.47 % Allowed : 25.21 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.98 (0.14), residues: 3780 helix: 2.31 (0.10), residues: 2548 sheet: -1.66 (0.34), residues: 220 loop : -0.59 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 426 HIS 0.003 0.001 HIS B 500 PHE 0.017 0.001 PHE A1013 TYR 0.020 0.001 TYR A 117 ARG 0.004 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 495 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.7793 (tp30) cc_final: 0.7399 (tp30) REVERT: A 132 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8334 (tp) REVERT: A 161 MET cc_start: 0.8214 (tpp) cc_final: 0.7627 (mmm) REVERT: A 378 ILE cc_start: 0.8260 (mm) cc_final: 0.7799 (mt) REVERT: A 382 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8512 (mtpt) REVERT: A 655 ASN cc_start: 0.8299 (t0) cc_final: 0.8057 (t0) REVERT: A 851 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.6829 (tpt-90) REVERT: A 900 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7565 (m-80) REVERT: A 1009 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8144 (mp) REVERT: B 131 GLU cc_start: 0.7765 (tp30) cc_final: 0.7406 (tp30) REVERT: B 161 MET cc_start: 0.8201 (tpp) cc_final: 0.7616 (mmm) REVERT: B 378 ILE cc_start: 0.8253 (mm) cc_final: 0.7860 (mp) REVERT: B 382 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8506 (mtpt) REVERT: B 655 ASN cc_start: 0.8304 (t0) cc_final: 0.8069 (t0) REVERT: B 851 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.6889 (tpt-90) REVERT: B 900 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: B 1009 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8140 (mp) REVERT: C 131 GLU cc_start: 0.7811 (tp30) cc_final: 0.7419 (tp30) REVERT: C 132 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8340 (tp) REVERT: C 161 MET cc_start: 0.8208 (tpp) cc_final: 0.7622 (mmm) REVERT: C 378 ILE cc_start: 0.8256 (mm) cc_final: 0.7867 (mp) REVERT: C 655 ASN cc_start: 0.8272 (t0) cc_final: 0.8044 (t0) REVERT: C 851 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.6831 (tpt-90) REVERT: C 900 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: D 131 GLU cc_start: 0.7813 (tp30) cc_final: 0.7397 (tp30) REVERT: D 132 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8292 (tp) REVERT: D 161 MET cc_start: 0.8231 (tpp) cc_final: 0.7630 (mmm) REVERT: D 851 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.6834 (tpt-90) outliers start: 160 outliers final: 64 residues processed: 606 average time/residue: 1.1545 time to fit residues: 849.0374 Evaluate side-chains 567 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 489 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 900 PHE Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 900 PHE Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 900 PHE Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 1024 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 276 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 333 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN B 46 GLN B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN C 294 ASN C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 ASN D 294 ASN D 676 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 30856 Z= 0.387 Angle : 0.557 6.909 42016 Z= 0.288 Chirality : 0.043 0.181 4856 Planarity : 0.004 0.049 5164 Dihedral : 7.660 79.512 4840 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 6.33 % Allowed : 24.28 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.54 (0.14), residues: 3780 helix: 1.95 (0.10), residues: 2552 sheet: -1.75 (0.34), residues: 220 loop : -0.71 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 426 HIS 0.005 0.001 HIS B 667 PHE 0.021 0.002 PHE B1013 TYR 0.022 0.002 TYR A 117 ARG 0.004 0.001 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 485 time to evaluate : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8495 (tttm) cc_final: 0.8188 (tmtp) REVERT: A 131 GLU cc_start: 0.7722 (tp30) cc_final: 0.7446 (tp30) REVERT: A 161 MET cc_start: 0.8289 (tpp) cc_final: 0.7638 (mmm) REVERT: A 219 MET cc_start: 0.8316 (mmm) cc_final: 0.8048 (mmt) REVERT: A 222 ASN cc_start: 0.7202 (m-40) cc_final: 0.6932 (m110) REVERT: A 382 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8554 (mtpt) REVERT: A 482 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7627 (tp) REVERT: A 507 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7834 (tpm170) REVERT: A 655 ASN cc_start: 0.8621 (t0) cc_final: 0.8050 (t0) REVERT: A 851 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7349 (tpt-90) REVERT: A 992 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8034 (pp30) REVERT: B 135 GLN cc_start: 0.7008 (mp10) cc_final: 0.6765 (mp10) REVERT: B 161 MET cc_start: 0.8288 (tpp) cc_final: 0.7633 (mmm) REVERT: B 222 ASN cc_start: 0.7220 (m-40) cc_final: 0.6947 (m110) REVERT: B 382 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8540 (mtpt) REVERT: B 482 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7641 (tp) REVERT: B 655 ASN cc_start: 0.8619 (t0) cc_final: 0.8048 (t0) REVERT: B 851 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.7349 (tpt-90) REVERT: B 992 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8033 (pp30) REVERT: C 131 GLU cc_start: 0.7733 (tp30) cc_final: 0.7447 (tp30) REVERT: C 161 MET cc_start: 0.8289 (tpp) cc_final: 0.7630 (mmm) REVERT: C 219 MET cc_start: 0.8310 (mmm) cc_final: 0.8039 (mmt) REVERT: C 222 ASN cc_start: 0.7209 (m-40) cc_final: 0.6929 (m110) REVERT: C 360 ARG cc_start: 0.7710 (tpt90) cc_final: 0.7503 (tpt90) REVERT: C 482 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7634 (tp) REVERT: C 655 ASN cc_start: 0.8617 (t0) cc_final: 0.8077 (t0) REVERT: C 851 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.7351 (tpt-90) REVERT: C 992 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8015 (pp30) REVERT: D 131 GLU cc_start: 0.7739 (tp30) cc_final: 0.7504 (tp30) REVERT: D 161 MET cc_start: 0.8307 (tpp) cc_final: 0.7637 (mmm) REVERT: D 219 MET cc_start: 0.8313 (mmm) cc_final: 0.8043 (mmt) REVERT: D 222 ASN cc_start: 0.7189 (m-40) cc_final: 0.6909 (m110) REVERT: D 248 ASP cc_start: 0.7242 (t0) cc_final: 0.7017 (t0) REVERT: D 482 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7606 (tp) REVERT: D 507 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7833 (tpm170) REVERT: D 655 ASN cc_start: 0.8662 (t0) cc_final: 0.8395 (t0) REVERT: D 851 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7351 (tpt-90) REVERT: D 992 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8020 (pp30) outliers start: 185 outliers final: 88 residues processed: 606 average time/residue: 1.1431 time to fit residues: 839.7700 Evaluate side-chains 577 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 473 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 676 ASN Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 911 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1024 VAL Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 3.9990 chunk 334 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 371 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 30856 Z= 0.410 Angle : 0.571 7.232 42016 Z= 0.297 Chirality : 0.044 0.196 4856 Planarity : 0.005 0.047 5164 Dihedral : 7.864 78.903 4840 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.85 % Allowed : 24.83 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.41 (0.14), residues: 3780 helix: 1.78 (0.10), residues: 2576 sheet: -1.38 (0.37), residues: 188 loop : -0.76 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 426 HIS 0.005 0.001 HIS B 185 PHE 0.020 0.002 PHE C 98 TYR 0.025 0.002 TYR B 117 ARG 0.004 0.001 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 483 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8509 (tttm) cc_final: 0.8126 (tttp) REVERT: A 135 GLN cc_start: 0.6978 (mp10) cc_final: 0.6737 (mp10) REVERT: A 161 MET cc_start: 0.8291 (tpp) cc_final: 0.7667 (mmm) REVERT: A 219 MET cc_start: 0.8339 (mmm) cc_final: 0.8056 (mmt) REVERT: A 222 ASN cc_start: 0.7193 (m-40) cc_final: 0.6931 (m110) REVERT: A 280 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: A 330 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7497 (pp20) REVERT: A 396 MET cc_start: 0.7790 (mtm) cc_final: 0.7356 (mtm) REVERT: A 507 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7641 (tpm170) REVERT: A 655 ASN cc_start: 0.8621 (t0) cc_final: 0.8275 (t0) REVERT: A 707 CYS cc_start: 0.7132 (m) cc_final: 0.6875 (t) REVERT: A 851 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7286 (tpt-90) REVERT: A 992 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8035 (pp30) REVERT: B 161 MET cc_start: 0.8287 (tpp) cc_final: 0.7667 (mmm) REVERT: B 222 ASN cc_start: 0.7195 (m-40) cc_final: 0.6926 (m110) REVERT: B 280 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: B 507 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7638 (tpm170) REVERT: B 655 ASN cc_start: 0.8617 (t0) cc_final: 0.8272 (t0) REVERT: B 707 CYS cc_start: 0.7124 (m) cc_final: 0.6874 (t) REVERT: B 851 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7283 (tpt-90) REVERT: B 992 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8035 (pp30) REVERT: C 96 LYS cc_start: 0.8547 (tmmm) cc_final: 0.8281 (tmtt) REVERT: C 98 PHE cc_start: 0.7364 (m-80) cc_final: 0.6995 (m-80) REVERT: C 135 GLN cc_start: 0.7004 (mp10) cc_final: 0.6769 (mp10) REVERT: C 161 MET cc_start: 0.8285 (tpp) cc_final: 0.7675 (mmm) REVERT: C 219 MET cc_start: 0.8338 (mmm) cc_final: 0.8059 (mmt) REVERT: C 222 ASN cc_start: 0.7199 (m-40) cc_final: 0.6927 (m110) REVERT: C 248 ASP cc_start: 0.7269 (t0) cc_final: 0.7053 (t0) REVERT: C 507 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7639 (tpm170) REVERT: C 655 ASN cc_start: 0.8636 (t0) cc_final: 0.8313 (t0) REVERT: C 707 CYS cc_start: 0.7117 (m) cc_final: 0.6865 (t) REVERT: C 851 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7288 (tpt-90) REVERT: C 992 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8024 (pp30) REVERT: D 161 MET cc_start: 0.8304 (tpp) cc_final: 0.7679 (mmm) REVERT: D 219 MET cc_start: 0.8335 (mmm) cc_final: 0.8072 (mmt) REVERT: D 222 ASN cc_start: 0.7175 (m-40) cc_final: 0.6915 (m110) REVERT: D 278 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7876 (ttt180) REVERT: D 507 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7642 (tpm170) REVERT: D 655 ASN cc_start: 0.8655 (t0) cc_final: 0.8372 (t0) REVERT: D 707 CYS cc_start: 0.7127 (m) cc_final: 0.6871 (t) REVERT: D 851 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.7288 (tpt-90) REVERT: D 992 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8025 (pp30) outliers start: 171 outliers final: 90 residues processed: 597 average time/residue: 1.2163 time to fit residues: 873.9926 Evaluate side-chains 578 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 472 time to evaluate : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 911 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain B residue 1052 THR Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1024 VAL Chi-restraints excluded: chain C residue 1052 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 382 LYS Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 911 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 992 GLN Chi-restraints excluded: chain D residue 1024 VAL Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 210 optimal weight: 0.0270 chunk 312 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 370 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 170 optimal weight: 0.3980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30856 Z= 0.165 Angle : 0.467 6.874 42016 Z= 0.243 Chirality : 0.037 0.162 4856 Planarity : 0.004 0.046 5164 Dihedral : 7.152 76.210 4832 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.51 % Allowed : 26.13 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.88 (0.14), residues: 3780 helix: 2.18 (0.10), residues: 2552 sheet: -1.28 (0.37), residues: 188 loop : -0.62 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 426 HIS 0.004 0.001 HIS C 389 PHE 0.022 0.001 PHE A1013 TYR 0.015 0.001 TYR D 621 ARG 0.004 0.000 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 503 time to evaluate : 3.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.7002 (m-40) cc_final: 0.6747 (m110) REVERT: A 248 ASP cc_start: 0.7192 (t0) cc_final: 0.6925 (t70) REVERT: A 378 ILE cc_start: 0.8321 (mm) cc_final: 0.7906 (mp) REVERT: A 851 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.6791 (tpt-90) REVERT: B 98 PHE cc_start: 0.7644 (m-80) cc_final: 0.7256 (m-80) REVERT: B 219 MET cc_start: 0.8282 (mmm) cc_final: 0.8032 (mmt) REVERT: B 222 ASN cc_start: 0.7014 (m-40) cc_final: 0.6766 (m110) REVERT: B 378 ILE cc_start: 0.8294 (mm) cc_final: 0.7876 (mp) REVERT: B 507 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7662 (tpm170) REVERT: B 851 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.6813 (tpt-90) REVERT: C 96 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8281 (tmtt) REVERT: C 98 PHE cc_start: 0.7417 (m-80) cc_final: 0.7104 (m-80) REVERT: C 222 ASN cc_start: 0.7033 (m-40) cc_final: 0.6779 (m110) REVERT: C 248 ASP cc_start: 0.7203 (t0) cc_final: 0.6953 (t70) REVERT: C 378 ILE cc_start: 0.8324 (mm) cc_final: 0.7908 (mp) REVERT: C 507 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7663 (tpm170) REVERT: C 707 CYS cc_start: 0.7066 (m) cc_final: 0.6839 (t) REVERT: C 851 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.6820 (tpt-90) REVERT: D 96 LYS cc_start: 0.8555 (tmmt) cc_final: 0.8274 (tmmt) REVERT: D 131 GLU cc_start: 0.7914 (mm-30) cc_final: 0.6818 (tp30) REVERT: D 219 MET cc_start: 0.8283 (mmm) cc_final: 0.8009 (mmt) REVERT: D 222 ASN cc_start: 0.6955 (m-40) cc_final: 0.6713 (m110) REVERT: D 378 ILE cc_start: 0.8321 (mm) cc_final: 0.7908 (mp) REVERT: D 707 CYS cc_start: 0.7064 (m) cc_final: 0.6837 (t) REVERT: D 851 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.6818 (tpt-90) outliers start: 132 outliers final: 63 residues processed: 594 average time/residue: 1.1915 time to fit residues: 864.8863 Evaluate side-chains 550 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 480 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 255 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 1024 VAL Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 911 MET Chi-restraints excluded: chain D residue 1024 VAL Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 34 optimal weight: 0.0470 chunk 290 optimal weight: 20.0000 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 437 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 306 GLN C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 437 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30856 Z= 0.221 Angle : 0.495 8.943 42016 Z= 0.258 Chirality : 0.039 0.213 4856 Planarity : 0.004 0.045 5164 Dihedral : 7.177 77.260 4832 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.00 % Allowed : 26.74 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.87 (0.14), residues: 3780 helix: 2.16 (0.10), residues: 2556 sheet: -1.29 (0.38), residues: 188 loop : -0.58 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 426 HIS 0.004 0.001 HIS B 185 PHE 0.024 0.001 PHE A1013 TYR 0.019 0.002 TYR D 621 ARG 0.004 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 475 time to evaluate : 3.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.7838 (mmm160) cc_final: 0.7548 (tpm-80) REVERT: A 219 MET cc_start: 0.8296 (mmm) cc_final: 0.8035 (mmt) REVERT: A 222 ASN cc_start: 0.7035 (m-40) cc_final: 0.6782 (m110) REVERT: A 280 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: A 378 ILE cc_start: 0.8334 (mm) cc_final: 0.7919 (mp) REVERT: A 655 ASN cc_start: 0.8515 (t0) cc_final: 0.8196 (t0) REVERT: A 851 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.6990 (tpt-90) REVERT: B 98 PHE cc_start: 0.7601 (m-80) cc_final: 0.7390 (m-80) REVERT: B 132 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8277 (tp) REVERT: B 167 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7552 (tpm-80) REVERT: B 222 ASN cc_start: 0.7029 (m-40) cc_final: 0.6786 (m110) REVERT: B 280 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7706 (mp10) REVERT: B 378 ILE cc_start: 0.8319 (mm) cc_final: 0.7882 (mp) REVERT: B 382 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8475 (mtmp) REVERT: B 507 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7663 (tpm170) REVERT: B 655 ASN cc_start: 0.8518 (t0) cc_final: 0.8192 (t0) REVERT: B 707 CYS cc_start: 0.7083 (m) cc_final: 0.6825 (t) REVERT: B 851 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.6992 (tpt-90) REVERT: C 96 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8234 (tmtt) REVERT: C 98 PHE cc_start: 0.7382 (m-80) cc_final: 0.7057 (m-80) REVERT: C 167 ARG cc_start: 0.7832 (mmm160) cc_final: 0.7541 (tpm-80) REVERT: C 222 ASN cc_start: 0.7048 (m-40) cc_final: 0.6801 (m110) REVERT: C 248 ASP cc_start: 0.7162 (t0) cc_final: 0.6951 (t70) REVERT: C 507 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7664 (tpm170) REVERT: C 655 ASN cc_start: 0.8537 (t0) cc_final: 0.8204 (t0) REVERT: C 707 CYS cc_start: 0.7053 (m) cc_final: 0.6819 (t) REVERT: C 851 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.6991 (tpt-90) REVERT: D 96 LYS cc_start: 0.8545 (tmmt) cc_final: 0.8236 (tmmt) REVERT: D 131 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7588 (mm-30) REVERT: D 167 ARG cc_start: 0.7845 (mmm160) cc_final: 0.7558 (tpm-80) REVERT: D 219 MET cc_start: 0.8293 (mmm) cc_final: 0.8029 (mmt) REVERT: D 222 ASN cc_start: 0.7017 (m-40) cc_final: 0.6772 (m110) REVERT: D 378 ILE cc_start: 0.8335 (mm) cc_final: 0.7920 (mp) REVERT: D 655 ASN cc_start: 0.8573 (t0) cc_final: 0.8259 (t0) REVERT: D 707 CYS cc_start: 0.7088 (m) cc_final: 0.6853 (t) REVERT: D 851 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7027 (tpt-90) outliers start: 117 outliers final: 71 residues processed: 560 average time/residue: 1.2264 time to fit residues: 827.4005 Evaluate side-chains 556 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 474 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 911 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain C residue 955 ILE Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 911 MET Chi-restraints excluded: chain D residue 955 ILE Chi-restraints excluded: chain D residue 1024 VAL Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 2.9990 chunk 354 optimal weight: 0.9980 chunk 323 optimal weight: 0.0770 chunk 344 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 270 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 311 optimal weight: 4.9990 chunk 326 optimal weight: 0.7980 chunk 343 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 437 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30856 Z= 0.160 Angle : 0.479 9.218 42016 Z= 0.249 Chirality : 0.038 0.198 4856 Planarity : 0.004 0.045 5164 Dihedral : 7.003 76.651 4832 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.83 % Allowed : 26.95 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.93 (0.14), residues: 3780 helix: 2.26 (0.10), residues: 2552 sheet: -1.70 (0.34), residues: 220 loop : -0.57 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 426 HIS 0.003 0.001 HIS D 185 PHE 0.024 0.001 PHE A1013 TYR 0.016 0.001 TYR D 772 ARG 0.004 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 479 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.7833 (mmm160) cc_final: 0.7606 (tpm-80) REVERT: A 186 TYR cc_start: 0.8529 (m-80) cc_final: 0.8081 (m-80) REVERT: A 219 MET cc_start: 0.8270 (mmm) cc_final: 0.8018 (mmt) REVERT: A 222 ASN cc_start: 0.6933 (m-40) cc_final: 0.6693 (m110) REVERT: A 280 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: A 378 ILE cc_start: 0.8301 (mm) cc_final: 0.7887 (mp) REVERT: A 655 ASN cc_start: 0.8337 (t0) cc_final: 0.8035 (t0) REVERT: A 851 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.6796 (tpt-90) REVERT: B 167 ARG cc_start: 0.7833 (mmm160) cc_final: 0.7610 (tpm-80) REVERT: B 219 MET cc_start: 0.8251 (mmm) cc_final: 0.7988 (mmt) REVERT: B 222 ASN cc_start: 0.6931 (m-40) cc_final: 0.6695 (m110) REVERT: B 378 ILE cc_start: 0.8260 (mm) cc_final: 0.7829 (mp) REVERT: B 382 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8474 (mtmp) REVERT: B 507 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7666 (tpm170) REVERT: B 851 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.6797 (tpt-90) REVERT: C 96 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8224 (tmtt) REVERT: C 98 PHE cc_start: 0.7357 (m-80) cc_final: 0.7011 (m-80) REVERT: C 167 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7603 (tpm-80) REVERT: C 222 ASN cc_start: 0.6936 (m-40) cc_final: 0.6699 (m110) REVERT: C 378 ILE cc_start: 0.8317 (mm) cc_final: 0.7903 (mp) REVERT: C 507 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7668 (tpm170) REVERT: C 707 CYS cc_start: 0.7023 (m) cc_final: 0.6800 (t) REVERT: C 851 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.6800 (tpt-90) REVERT: D 96 LYS cc_start: 0.8508 (tmmt) cc_final: 0.8196 (tmmt) REVERT: D 167 ARG cc_start: 0.7837 (mmm160) cc_final: 0.7612 (tpm-80) REVERT: D 219 MET cc_start: 0.8268 (mmm) cc_final: 0.8001 (mmt) REVERT: D 222 ASN cc_start: 0.6974 (m-40) cc_final: 0.6730 (m110) REVERT: D 378 ILE cc_start: 0.8309 (mm) cc_final: 0.7900 (mp) REVERT: D 707 CYS cc_start: 0.7015 (m) cc_final: 0.6793 (t) REVERT: D 851 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.6798 (tpt-90) outliers start: 112 outliers final: 69 residues processed: 561 average time/residue: 1.1730 time to fit residues: 795.6342 Evaluate side-chains 557 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 479 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 911 MET Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 911 MET Chi-restraints excluded: chain D residue 1024 VAL Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.0010 chunk 364 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 253 optimal weight: 1.9990 chunk 382 optimal weight: 7.9990 chunk 352 optimal weight: 0.4980 chunk 304 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 235 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN D 294 ASN D 437 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30856 Z= 0.196 Angle : 0.507 9.953 42016 Z= 0.262 Chirality : 0.039 0.228 4856 Planarity : 0.004 0.045 5164 Dihedral : 7.017 77.255 4832 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.11 % Allowed : 28.08 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.88 (0.14), residues: 3780 helix: 2.21 (0.10), residues: 2556 sheet: -1.74 (0.34), residues: 220 loop : -0.55 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 426 HIS 0.004 0.001 HIS B 185 PHE 0.027 0.001 PHE A 44 TYR 0.020 0.001 TYR D 772 ARG 0.005 0.000 ARG C 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 484 time to evaluate : 3.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.7831 (mmm160) cc_final: 0.7606 (tpm-80) REVERT: A 186 TYR cc_start: 0.8538 (m-80) cc_final: 0.8096 (m-80) REVERT: A 219 MET cc_start: 0.8269 (mmm) cc_final: 0.8013 (mmt) REVERT: A 222 ASN cc_start: 0.6970 (m-40) cc_final: 0.6730 (m110) REVERT: A 280 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7690 (mp10) REVERT: A 378 ILE cc_start: 0.8325 (mm) cc_final: 0.7910 (mp) REVERT: A 655 ASN cc_start: 0.8417 (t0) cc_final: 0.8128 (t0) REVERT: A 851 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.6938 (tpt-90) REVERT: B 167 ARG cc_start: 0.7837 (mmm160) cc_final: 0.7595 (tpm-80) REVERT: B 219 MET cc_start: 0.8266 (mmm) cc_final: 0.8004 (mmt) REVERT: B 222 ASN cc_start: 0.6970 (m-40) cc_final: 0.6732 (m110) REVERT: B 280 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: B 378 ILE cc_start: 0.8306 (mm) cc_final: 0.7874 (mp) REVERT: B 382 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8484 (mtmp) REVERT: B 507 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7669 (tpm170) REVERT: B 655 ASN cc_start: 0.8560 (t0) cc_final: 0.8250 (t0) REVERT: B 851 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.6936 (tpt-90) REVERT: C 96 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8145 (tmtt) REVERT: C 98 PHE cc_start: 0.7365 (m-80) cc_final: 0.6914 (m-80) REVERT: C 167 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7592 (tpm-80) REVERT: C 219 MET cc_start: 0.8264 (mmm) cc_final: 0.8032 (mmt) REVERT: C 222 ASN cc_start: 0.6969 (m-40) cc_final: 0.6734 (m110) REVERT: C 507 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7670 (tpm170) REVERT: C 655 ASN cc_start: 0.8511 (t0) cc_final: 0.8197 (t0) REVERT: C 707 CYS cc_start: 0.7035 (m) cc_final: 0.6807 (t) REVERT: C 851 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.6953 (tpt-90) REVERT: D 96 LYS cc_start: 0.8497 (tmmt) cc_final: 0.8178 (tmmt) REVERT: D 167 ARG cc_start: 0.7831 (mmm160) cc_final: 0.7608 (tpm-80) REVERT: D 219 MET cc_start: 0.8276 (mmm) cc_final: 0.8013 (mmt) REVERT: D 222 ASN cc_start: 0.6973 (m-40) cc_final: 0.6738 (m110) REVERT: D 707 CYS cc_start: 0.7037 (m) cc_final: 0.6807 (t) REVERT: D 851 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.6953 (tpt-90) outliers start: 91 outliers final: 68 residues processed: 548 average time/residue: 1.1750 time to fit residues: 774.8978 Evaluate side-chains 549 residues out of total 3432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 471 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 911 MET Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 808 TYR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 911 MET Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 491 ASP Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 808 TYR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 911 MET Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 491 ASP Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 808 TYR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 911 MET Chi-restraints excluded: chain D residue 1024 VAL Chi-restraints excluded: chain D residue 1052 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 0.6980 chunk 324 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 280 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 305 optimal weight: 0.0980 chunk 127 optimal weight: 3.9990 chunk 313 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 437 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.134979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103705 restraints weight = 47293.094| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.72 r_work: 0.3188 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 30856 Z= 0.211 Angle : 0.637 59.135 42016 Z= 0.352 Chirality : 0.043 1.383 4856 Planarity : 0.004 0.044 5164 Dihedral : 7.016 77.228 4832 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.32 % Allowed : 28.08 % Favored : 68.60 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.35 % 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: 1.89 (0.14), residues: 3780 helix: 2.22 (0.10), residues: 2556 sheet: -1.74 (0.34), residues: 220 loop : -0.55 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 426 HIS 0.004 0.001 HIS B 185 PHE 0.024 0.001 PHE A1013 TYR 0.017 0.001 TYR D 621 ARG 0.004 0.000 ARG C 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12909.00 seconds wall clock time: 229 minutes 32.07 seconds (13772.07 seconds total)