Starting phenix.real_space_refine on Mon May 4 02:39:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9efh_47973/05_2026/9efh_47973.cif Found real_map, /net/cci-nas-00/data/ceres_data/9efh_47973/05_2026/9efh_47973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9efh_47973/05_2026/9efh_47973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9efh_47973/05_2026/9efh_47973.map" model { file = "/net/cci-nas-00/data/ceres_data/9efh_47973/05_2026/9efh_47973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9efh_47973/05_2026/9efh_47973.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 10764 2.51 5 N 2976 2.21 5 O 3180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17013 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5643 Classifications: {'peptide': 711} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 681} Chain breaks: 4 Chain: "B" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5643 Classifications: {'peptide': 711} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 681} Chain breaks: 4 Chain: "C" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5643 Classifications: {'peptide': 711} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 681} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.19, per 1000 atoms: 0.25 Number of scatterers: 17013 At special positions: 0 Unit cell: (117.48, 123.42, 195.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 3180 8.00 N 2976 7.00 C 10764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.04 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG D 1 " - " ASN A 398 " " NAG E 1 " - " ASN B 398 " " NAG F 1 " - " ASN C 398 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 855.9 milliseconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3996 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 29 sheets defined 39.2% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 87 through 106 Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.507A pdb=" N PHE A 182 " --> pdb=" O TYR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 303 through 310 removed outlier: 4.032A pdb=" N GLY A 306 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N HIS A 308 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR A 309 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 501 through 546 removed outlier: 3.785A pdb=" N GLU A 530 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU A 545 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 669 through 675 removed outlier: 3.800A pdb=" N ILE A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 691 removed outlier: 4.181A pdb=" N TYR A 689 " --> pdb=" O PRO A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 724 Processing helix chain 'A' and resid 726 through 741 removed outlier: 3.524A pdb=" N ALA A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 772 removed outlier: 3.651A pdb=" N VAL A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 803 Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'A' and resid 838 through 862 removed outlier: 3.566A pdb=" N LYS A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 106 Processing helix chain 'B' and resid 180 through 183 Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 303 through 307 removed outlier: 4.069A pdb=" N GLY B 306 " --> pdb=" O TYR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 501 through 546 removed outlier: 3.804A pdb=" N GLU B 530 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU B 545 " --> pdb=" O GLU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 669 through 675 removed outlier: 3.756A pdb=" N ILE B 675 " --> pdb=" O ILE B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 691 removed outlier: 4.179A pdb=" N TYR B 689 " --> pdb=" O PRO B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 724 Processing helix chain 'B' and resid 726 through 741 removed outlier: 3.936A pdb=" N GLY B 741 " --> pdb=" O ALA B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 772 removed outlier: 3.658A pdb=" N VAL B 752 " --> pdb=" O ALA B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 803 Processing helix chain 'B' and resid 804 through 810 Processing helix chain 'B' and resid 838 through 862 removed outlier: 3.548A pdb=" N LYS B 862 " --> pdb=" O ARG B 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 106 Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 303 through 310 removed outlier: 4.066A pdb=" N GLY C 306 " --> pdb=" O TYR C 303 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N HIS C 308 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR C 309 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 411 through 429 Processing helix chain 'C' and resid 459 through 466 Processing helix chain 'C' and resid 501 through 546 removed outlier: 3.783A pdb=" N GLU C 530 " --> pdb=" O ILE C 526 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU C 545 " --> pdb=" O GLU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 669 through 675 removed outlier: 3.768A pdb=" N ILE C 675 " --> pdb=" O ILE C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 691 removed outlier: 4.173A pdb=" N TYR C 689 " --> pdb=" O PRO C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 724 Processing helix chain 'C' and resid 726 through 741 removed outlier: 3.922A pdb=" N GLY C 741 " --> pdb=" O ALA C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 772 removed outlier: 3.523A pdb=" N VAL C 752 " --> pdb=" O ALA C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 803 Processing helix chain 'C' and resid 804 through 810 Processing helix chain 'C' and resid 838 through 862 removed outlier: 3.548A pdb=" N LYS C 862 " --> pdb=" O ARG C 858 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.523A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 563 removed outlier: 3.687A pdb=" N THR B 665 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 433 through 435 removed outlier: 3.655A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 443 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN A 398 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU A 374 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY A 145 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A 376 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR A 143 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 13.763A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 191 Processing sheet with id=AA5, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.296A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR A 340 " --> pdb=" O GLY A 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA7, first strand: chain 'A' and resid 210 through 214 Processing sheet with id=AA8, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AA9, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.548A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 665 through 666 removed outlier: 6.543A pdb=" N THR A 665 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AB3, first strand: chain 'B' and resid 559 through 563 removed outlier: 3.675A pdb=" N THR C 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 433 through 435 removed outlier: 3.627A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 443 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN B 398 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU B 374 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY B 145 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU B 376 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR B 143 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 13.788A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 191 Processing sheet with id=AB6, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.354A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AB8, first strand: chain 'B' and resid 210 through 214 Processing sheet with id=AB9, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AC1, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC2, first strand: chain 'B' and resid 638 through 643 removed outlier: 3.551A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AC4, first strand: chain 'C' and resid 433 through 435 removed outlier: 3.668A pdb=" N PHE C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C 443 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN C 398 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU C 374 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY C 145 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU C 376 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR C 143 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 13.790A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 185 through 191 Processing sheet with id=AC6, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.329A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AC8, first strand: chain 'C' and resid 210 through 214 Processing sheet with id=AC9, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AD1, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD2, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.555A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 938 hydrogen bonds defined for protein. 2670 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: 3.80 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5637 1.34 - 1.46: 3996 1.46 - 1.58: 7620 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 17409 Sorted by residual: bond pdb=" CB PHE C 793 " pdb=" CG PHE C 793 " ideal model delta sigma weight residual 1.502 1.524 -0.022 2.30e-02 1.89e+03 9.01e-01 bond pdb=" C ARG B 523 " pdb=" O ARG B 523 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.17e-02 7.31e+03 8.68e-01 bond pdb=" C ALA C 527 " pdb=" O ALA C 527 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.19e-02 7.06e+03 8.50e-01 bond pdb=" C ARG C 523 " pdb=" O ARG C 523 " ideal model delta sigma weight residual 1.237 1.247 -0.011 1.17e-02 7.31e+03 8.40e-01 bond pdb=" C ARG A 523 " pdb=" O ARG A 523 " ideal model delta sigma weight residual 1.237 1.247 -0.010 1.17e-02 7.31e+03 8.05e-01 ... (remaining 17404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 23367 1.92 - 3.83: 221 3.83 - 5.75: 14 5.75 - 7.66: 5 7.66 - 9.58: 3 Bond angle restraints: 23610 Sorted by residual: angle pdb=" CB MET A 806 " pdb=" CG MET A 806 " pdb=" SD MET A 806 " ideal model delta sigma weight residual 112.70 122.28 -9.58 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CA MET C 856 " pdb=" CB MET C 856 " pdb=" CG MET C 856 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.47e+00 angle pdb=" CA MET A 856 " pdb=" CB MET A 856 " pdb=" CG MET A 856 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.02e+00 angle pdb=" CA MET B 856 " pdb=" CB MET B 856 " pdb=" CG MET B 856 " ideal model delta sigma weight residual 114.10 119.66 -5.56 2.00e+00 2.50e-01 7.74e+00 angle pdb=" CB MET C 806 " pdb=" CG MET C 806 " pdb=" SD MET C 806 " ideal model delta sigma weight residual 112.70 121.04 -8.34 3.00e+00 1.11e-01 7.73e+00 ... (remaining 23605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 8995 17.61 - 35.23: 994 35.23 - 52.84: 342 52.84 - 70.46: 72 70.46 - 88.07: 22 Dihedral angle restraints: 10425 sinusoidal: 4206 harmonic: 6219 Sorted by residual: dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS B 271 " pdb=" CB CYS B 271 " ideal model delta sinusoidal sigma weight residual 93.00 33.73 59.27 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CB CYS B 364 " pdb=" SG CYS B 364 " pdb=" SG CYS B 412 " pdb=" CB CYS B 412 " ideal model delta sinusoidal sigma weight residual -86.00 -129.58 43.58 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS C 364 " pdb=" SG CYS C 364 " pdb=" SG CYS C 412 " pdb=" CB CYS C 412 " ideal model delta sinusoidal sigma weight residual -86.00 -129.44 43.44 1 1.00e+01 1.00e-02 2.63e+01 ... (remaining 10422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1594 0.027 - 0.053: 619 0.053 - 0.080: 229 0.080 - 0.107: 114 0.107 - 0.133: 42 Chirality restraints: 2598 Sorted by residual: chirality pdb=" CB ILE B 847 " pdb=" CA ILE B 847 " pdb=" CG1 ILE B 847 " pdb=" CG2 ILE B 847 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL C 273 " pdb=" N VAL C 273 " pdb=" C VAL C 273 " pdb=" CB VAL C 273 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE C 582 " pdb=" N ILE C 582 " pdb=" C ILE C 582 " pdb=" CB ILE C 582 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 2595 not shown) Planarity restraints: 3069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 773 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.50e+00 pdb=" N PRO C 774 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 774 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 774 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 773 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO A 774 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 774 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 774 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 773 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO B 774 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 774 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 774 " 0.026 5.00e-02 4.00e+02 ... (remaining 3066 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1201 2.74 - 3.28: 15614 3.28 - 3.82: 28264 3.82 - 4.36: 33774 4.36 - 4.90: 58557 Nonbonded interactions: 137410 Sorted by model distance: nonbonded pdb=" O GLN B 802 " pdb=" NH2 ARG C 858 " model vdw 2.200 3.120 nonbonded pdb=" NH2 ARG A 858 " pdb=" O GLN C 802 " model vdw 2.215 3.120 nonbonded pdb=" O THR C 250 " pdb=" OG1 THR C 250 " model vdw 2.216 3.040 nonbonded pdb=" O THR B 250 " pdb=" OG1 THR B 250 " model vdw 2.216 3.040 nonbonded pdb=" O THR A 250 " pdb=" OG1 THR A 250 " model vdw 2.217 3.040 ... (remaining 137405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 9.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.720 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.002 0.025 17427 Z= 0.115 Angle : 0.496 9.575 23652 Z= 0.273 Chirality : 0.038 0.133 2598 Planarity : 0.004 0.047 3066 Dihedral : 17.026 88.073 6393 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.92 % Allowed : 21.32 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.18), residues: 2103 helix: 3.13 (0.19), residues: 726 sheet: 1.04 (0.22), residues: 552 loop : -0.07 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 406 TYR 0.010 0.001 TYR A 849 PHE 0.018 0.001 PHE A 793 TRP 0.018 0.002 TRP A 528 HIS 0.003 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00229 (17409) covalent geometry : angle 0.49445 (23610) SS BOND : bond 0.00320 ( 12) SS BOND : angle 0.89373 ( 24) hydrogen bonds : bond 0.14052 ( 896) hydrogen bonds : angle 6.07064 ( 2670) link_BETA1-4 : bond 0.00283 ( 3) link_BETA1-4 : angle 0.92584 ( 9) link_NAG-ASN : bond 0.00300 ( 3) link_NAG-ASN : angle 0.98567 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: A 305 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5366 (tm-30) REVERT: A 519 ASP cc_start: 0.7552 (m-30) cc_final: 0.7317 (m-30) REVERT: A 563 MET cc_start: 0.9334 (mmm) cc_final: 0.8569 (mmm) REVERT: A 607 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: A 704 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8297 (mm-30) REVERT: A 742 MET cc_start: 0.5314 (tpp) cc_final: 0.4514 (ptp) REVERT: A 799 MET cc_start: 0.7068 (mmp) cc_final: 0.6690 (mmm) REVERT: A 850 MET cc_start: 0.6155 (mmm) cc_final: 0.4980 (mmm) REVERT: B 128 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7246 (mm-30) REVERT: B 305 GLU cc_start: 0.5847 (OUTLIER) cc_final: 0.5349 (tm-30) REVERT: B 519 ASP cc_start: 0.7572 (m-30) cc_final: 0.7279 (m-30) REVERT: B 626 THR cc_start: 0.8554 (p) cc_final: 0.8296 (p) REVERT: B 742 MET cc_start: 0.5446 (tpp) cc_final: 0.4451 (ptp) REVERT: B 799 MET cc_start: 0.7043 (mmp) cc_final: 0.6782 (mmm) REVERT: B 806 MET cc_start: 0.5341 (tpp) cc_final: 0.4255 (tpt) REVERT: B 856 MET cc_start: 0.5897 (ppp) cc_final: 0.4983 (mmp) REVERT: C 187 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: C 305 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5349 (tm-30) REVERT: C 742 MET cc_start: 0.5123 (tpp) cc_final: 0.4280 (ptp) REVERT: C 806 MET cc_start: 0.5511 (tpp) cc_final: 0.4616 (tpt) REVERT: C 856 MET cc_start: 0.6251 (ppp) cc_final: 0.5220 (ttp) outliers start: 52 outliers final: 33 residues processed: 247 average time/residue: 0.6292 time to fit residues: 173.0839 Evaluate side-chains 247 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 814 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 512 HIS C 126 GLN C 512 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.172204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114882 restraints weight = 17640.018| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.96 r_work: 0.3102 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17427 Z= 0.198 Angle : 0.577 7.572 23652 Z= 0.315 Chirality : 0.044 0.161 2598 Planarity : 0.005 0.055 3066 Dihedral : 7.457 57.179 2572 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.84 % Allowed : 17.79 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.18), residues: 2103 helix: 2.92 (0.18), residues: 753 sheet: 0.98 (0.21), residues: 591 loop : -0.29 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 562 TYR 0.010 0.002 TYR A 849 PHE 0.022 0.002 PHE A 287 TRP 0.011 0.002 TRP B 539 HIS 0.004 0.001 HIS C 433 Details of bonding type rmsd covalent geometry : bond 0.00461 (17409) covalent geometry : angle 0.57586 (23610) SS BOND : bond 0.00594 ( 12) SS BOND : angle 1.05281 ( 24) hydrogen bonds : bond 0.05937 ( 896) hydrogen bonds : angle 4.98422 ( 2670) link_BETA1-4 : bond 0.00061 ( 3) link_BETA1-4 : angle 1.00810 ( 9) link_NAG-ASN : bond 0.00020 ( 3) link_NAG-ASN : angle 1.14085 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 207 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: A 305 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5486 (tm-30) REVERT: A 374 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: A 421 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8287 (mmm) REVERT: A 465 VAL cc_start: 0.7764 (OUTLIER) cc_final: 0.7507 (m) REVERT: A 584 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7518 (mp-120) REVERT: A 704 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8208 (mm-30) REVERT: A 742 MET cc_start: 0.5287 (tpp) cc_final: 0.4492 (ptp) REVERT: A 771 MET cc_start: 0.7334 (mmm) cc_final: 0.7116 (mtm) REVERT: A 858 ARG cc_start: 0.4959 (OUTLIER) cc_final: 0.4250 (mmp-170) REVERT: B 183 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6184 (mpm) REVERT: B 305 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5425 (tm-30) REVERT: B 374 GLU cc_start: 0.8349 (mp0) cc_final: 0.7797 (pm20) REVERT: B 465 VAL cc_start: 0.7870 (OUTLIER) cc_final: 0.7638 (m) REVERT: B 704 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8214 (mm-30) REVERT: B 742 MET cc_start: 0.5473 (tpp) cc_final: 0.4628 (ptp) REVERT: C 181 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6703 (pm20) REVERT: C 195 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: C 304 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6051 (ptm160) REVERT: C 305 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.4903 (tm-30) REVERT: C 360 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6353 (mpp-170) REVERT: C 465 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7574 (m) REVERT: C 742 MET cc_start: 0.5186 (tpp) cc_final: 0.4307 (ptp) REVERT: C 771 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7286 (mtm) outliers start: 104 outliers final: 54 residues processed: 284 average time/residue: 0.6059 time to fit residues: 191.3765 Evaluate side-chains 278 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 205 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 771 MET Chi-restraints excluded: chain C residue 814 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 96 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 GLN B 512 HIS C 512 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.170802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112602 restraints weight = 17794.149| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.12 r_work: 0.3088 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17427 Z= 0.248 Angle : 0.624 8.333 23652 Z= 0.341 Chirality : 0.047 0.193 2598 Planarity : 0.005 0.054 3066 Dihedral : 7.480 59.566 2552 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 6.51 % Allowed : 16.89 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.18), residues: 2103 helix: 2.76 (0.18), residues: 753 sheet: 0.90 (0.21), residues: 591 loop : -0.47 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 562 TYR 0.013 0.002 TYR A 849 PHE 0.026 0.002 PHE C 287 TRP 0.012 0.002 TRP A 354 HIS 0.005 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00586 (17409) covalent geometry : angle 0.62195 (23610) SS BOND : bond 0.00812 ( 12) SS BOND : angle 1.36994 ( 24) hydrogen bonds : bond 0.06294 ( 896) hydrogen bonds : angle 4.91419 ( 2670) link_BETA1-4 : bond 0.00286 ( 3) link_BETA1-4 : angle 1.13472 ( 9) link_NAG-ASN : bond 0.00072 ( 3) link_NAG-ASN : angle 1.14761 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 207 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: A 305 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5425 (tm-30) REVERT: A 349 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8472 (mtpt) REVERT: A 373 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: A 374 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: A 405 SER cc_start: 0.8127 (m) cc_final: 0.7912 (m) REVERT: A 415 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7407 (tptm) REVERT: A 421 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8320 (mmm) REVERT: A 465 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7527 (m) REVERT: A 584 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7524 (mp-120) REVERT: A 607 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7043 (mm-30) REVERT: A 704 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8272 (mm-30) REVERT: A 742 MET cc_start: 0.5361 (tpp) cc_final: 0.4480 (ptp) REVERT: B 183 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6230 (mpm) REVERT: B 305 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5506 (tm-30) REVERT: B 415 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7433 (mmmt) REVERT: B 465 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7660 (m) REVERT: B 704 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8243 (mm-30) REVERT: B 742 MET cc_start: 0.5529 (tpp) cc_final: 0.4671 (ptp) REVERT: C 304 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6072 (ptm160) REVERT: C 305 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.4974 (tm-30) REVERT: C 360 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6393 (mpp-170) REVERT: C 405 SER cc_start: 0.8089 (m) cc_final: 0.7586 (p) REVERT: C 415 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7371 (tptm) REVERT: C 465 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7591 (m) REVERT: C 742 MET cc_start: 0.5163 (tpp) cc_final: 0.4315 (ptp) REVERT: C 771 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7348 (mtm) outliers start: 116 outliers final: 69 residues processed: 296 average time/residue: 0.6086 time to fit residues: 200.6791 Evaluate side-chains 288 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 197 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 248 HIS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 248 HIS Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 771 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 116 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 205 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 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 100 HIS ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 100 HIS B 512 HIS C 512 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.173893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114953 restraints weight = 17841.128| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.72 r_work: 0.3179 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17427 Z= 0.115 Angle : 0.479 6.083 23652 Z= 0.261 Chirality : 0.040 0.142 2598 Planarity : 0.004 0.053 3066 Dihedral : 6.708 56.258 2548 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.05 % Allowed : 19.08 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.18), residues: 2103 helix: 3.04 (0.19), residues: 735 sheet: 0.98 (0.22), residues: 570 loop : -0.17 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 428 TYR 0.011 0.001 TYR A 849 PHE 0.020 0.001 PHE C 793 TRP 0.011 0.001 TRP C 528 HIS 0.003 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00239 (17409) covalent geometry : angle 0.47779 (23610) SS BOND : bond 0.00394 ( 12) SS BOND : angle 0.73311 ( 24) hydrogen bonds : bond 0.04809 ( 896) hydrogen bonds : angle 4.63679 ( 2670) link_BETA1-4 : bond 0.00375 ( 3) link_BETA1-4 : angle 0.96397 ( 9) link_NAG-ASN : bond 0.00243 ( 3) link_NAG-ASN : angle 0.94316 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 197 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASN cc_start: 0.5638 (OUTLIER) cc_final: 0.5421 (m110) REVERT: A 195 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: A 374 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: A 415 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7281 (tttm) REVERT: A 421 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8174 (mmm) REVERT: A 584 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7531 (mp-120) REVERT: A 607 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7036 (mm-30) REVERT: A 742 MET cc_start: 0.5263 (tpp) cc_final: 0.4587 (ptp) REVERT: A 858 ARG cc_start: 0.4996 (OUTLIER) cc_final: 0.4188 (mmp-170) REVERT: B 183 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6311 (mpm) REVERT: B 305 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5420 (tm-30) REVERT: B 415 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7394 (mmmt) REVERT: B 587 MET cc_start: 0.9443 (mtp) cc_final: 0.9197 (mtp) REVERT: B 607 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: B 704 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: B 742 MET cc_start: 0.5389 (tpp) cc_final: 0.4735 (ptm) REVERT: B 771 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7163 (mtm) REVERT: B 806 MET cc_start: 0.4991 (tpp) cc_final: 0.3965 (tpt) REVERT: C 374 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: C 411 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6279 (t70) REVERT: C 415 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7339 (tptm) REVERT: C 607 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7062 (mm-30) REVERT: C 742 MET cc_start: 0.5090 (tpp) cc_final: 0.4455 (ptp) REVERT: C 806 MET cc_start: 0.5518 (tpp) cc_final: 0.4617 (tpt) outliers start: 90 outliers final: 49 residues processed: 261 average time/residue: 0.5980 time to fit residues: 174.3532 Evaluate side-chains 263 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 196 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 814 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 132 optimal weight: 0.0000 chunk 207 optimal weight: 7.9990 overall best weight: 1.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 512 HIS C 512 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.171683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112168 restraints weight = 17714.674| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.72 r_work: 0.3135 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17427 Z= 0.190 Angle : 0.560 7.539 23652 Z= 0.304 Chirality : 0.043 0.161 2598 Planarity : 0.005 0.054 3066 Dihedral : 6.615 58.042 2538 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.39 % Allowed : 18.01 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.18), residues: 2103 helix: 2.96 (0.19), residues: 735 sheet: 0.92 (0.21), residues: 591 loop : -0.35 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.011 0.002 TYR A 849 PHE 0.022 0.002 PHE C 287 TRP 0.011 0.002 TRP A 539 HIS 0.004 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00444 (17409) covalent geometry : angle 0.55812 (23610) SS BOND : bond 0.00650 ( 12) SS BOND : angle 1.15401 ( 24) hydrogen bonds : bond 0.05591 ( 896) hydrogen bonds : angle 4.69025 ( 2670) link_BETA1-4 : bond 0.00041 ( 3) link_BETA1-4 : angle 1.02025 ( 9) link_NAG-ASN : bond 0.00017 ( 3) link_NAG-ASN : angle 1.09275 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 195 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: A 305 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5424 (tm-30) REVERT: A 374 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: A 405 SER cc_start: 0.8084 (m) cc_final: 0.7870 (m) REVERT: A 415 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7399 (tptm) REVERT: A 421 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8275 (mmm) REVERT: A 465 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7513 (m) REVERT: A 584 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7532 (mp-120) REVERT: A 607 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7074 (mm-30) REVERT: A 704 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8219 (mm-30) REVERT: A 742 MET cc_start: 0.5300 (tpp) cc_final: 0.4627 (ptp) REVERT: B 183 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6249 (mpm) REVERT: B 305 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5456 (tm-30) REVERT: B 374 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: B 465 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7610 (m) REVERT: B 587 MET cc_start: 0.9444 (mtp) cc_final: 0.9203 (mtp) REVERT: B 704 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8151 (mm-30) REVERT: B 742 MET cc_start: 0.5356 (tpp) cc_final: 0.4664 (ptp) REVERT: C 304 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6045 (ptm160) REVERT: C 305 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5019 (tm-30) REVERT: C 360 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6342 (mpp-170) REVERT: C 374 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: C 405 SER cc_start: 0.8043 (m) cc_final: 0.7542 (p) REVERT: C 415 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7408 (tptm) REVERT: C 465 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.7600 (m) REVERT: C 607 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7115 (mm-30) REVERT: C 742 MET cc_start: 0.5098 (tpp) cc_final: 0.4464 (ptp) outliers start: 96 outliers final: 57 residues processed: 271 average time/residue: 0.6097 time to fit residues: 184.4655 Evaluate side-chains 271 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 193 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 814 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 146 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 204 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 117 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS C 100 HIS C 512 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.174248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115326 restraints weight = 17729.673| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.72 r_work: 0.3189 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17427 Z= 0.110 Angle : 0.476 7.609 23652 Z= 0.258 Chirality : 0.039 0.143 2598 Planarity : 0.004 0.054 3066 Dihedral : 6.141 55.818 2538 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.60 % Allowed : 18.80 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.18), residues: 2103 helix: 3.11 (0.19), residues: 735 sheet: 0.96 (0.22), residues: 570 loop : -0.11 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 428 TYR 0.012 0.001 TYR A 849 PHE 0.021 0.001 PHE C 793 TRP 0.012 0.001 TRP C 528 HIS 0.003 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00231 (17409) covalent geometry : angle 0.47484 (23610) SS BOND : bond 0.00376 ( 12) SS BOND : angle 0.69560 ( 24) hydrogen bonds : bond 0.04608 ( 896) hydrogen bonds : angle 4.53230 ( 2670) link_BETA1-4 : bond 0.00279 ( 3) link_BETA1-4 : angle 0.92527 ( 9) link_NAG-ASN : bond 0.00214 ( 3) link_NAG-ASN : angle 0.96864 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 204 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8101 (pm20) cc_final: 0.7838 (mp0) REVERT: A 305 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5433 (tm-30) REVERT: A 374 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: A 415 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7301 (tttm) REVERT: A 421 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8178 (mmm) REVERT: A 519 ASP cc_start: 0.7544 (m-30) cc_final: 0.7232 (m-30) REVERT: A 584 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7512 (mp-120) REVERT: A 607 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7043 (mm-30) REVERT: A 626 THR cc_start: 0.8615 (p) cc_final: 0.8270 (m) REVERT: A 742 MET cc_start: 0.5286 (tpp) cc_final: 0.4670 (ptt) REVERT: A 806 MET cc_start: 0.5389 (tpp) cc_final: 0.4252 (tpt) REVERT: A 858 ARG cc_start: 0.4885 (OUTLIER) cc_final: 0.4058 (mmp-170) REVERT: B 183 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6256 (mpm) REVERT: B 374 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: B 465 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7659 (m) REVERT: B 519 ASP cc_start: 0.7549 (m-30) cc_final: 0.7245 (m-30) REVERT: B 607 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: B 704 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8118 (mm-30) REVERT: B 742 MET cc_start: 0.5290 (tpp) cc_final: 0.4611 (ptp) REVERT: B 806 MET cc_start: 0.5119 (tpp) cc_final: 0.4071 (tpt) REVERT: C 304 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6070 (ptm160) REVERT: C 305 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.4970 (tm-30) REVERT: C 374 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: C 411 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6327 (t70) REVERT: C 415 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7337 (tptm) REVERT: C 465 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7557 (m) REVERT: C 607 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7066 (mm-30) REVERT: C 742 MET cc_start: 0.5127 (tpp) cc_final: 0.4572 (ptp) REVERT: C 806 MET cc_start: 0.5327 (tpp) cc_final: 0.4588 (tpt) outliers start: 82 outliers final: 49 residues processed: 265 average time/residue: 0.5652 time to fit residues: 167.7030 Evaluate side-chains 268 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 200 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 857 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 195 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 0.0170 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 203 optimal weight: 20.0000 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS C 512 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.175668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118541 restraints weight = 17680.692| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.93 r_work: 0.3175 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17427 Z= 0.095 Angle : 0.450 7.743 23652 Z= 0.243 Chirality : 0.038 0.144 2598 Planarity : 0.004 0.054 3066 Dihedral : 5.666 54.667 2532 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.38 % Allowed : 19.08 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.18), residues: 2103 helix: 3.22 (0.19), residues: 735 sheet: 0.95 (0.22), residues: 570 loop : -0.04 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 428 TYR 0.010 0.001 TYR B 849 PHE 0.019 0.001 PHE A 793 TRP 0.013 0.001 TRP C 369 HIS 0.003 0.000 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00190 (17409) covalent geometry : angle 0.44898 (23610) SS BOND : bond 0.00308 ( 12) SS BOND : angle 0.59138 ( 24) hydrogen bonds : bond 0.04197 ( 896) hydrogen bonds : angle 4.42167 ( 2670) link_BETA1-4 : bond 0.00320 ( 3) link_BETA1-4 : angle 0.96007 ( 9) link_NAG-ASN : bond 0.00211 ( 3) link_NAG-ASN : angle 1.03889 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 205 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: A 305 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5423 (tm-30) REVERT: A 374 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: A 415 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7224 (tttm) REVERT: A 421 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8109 (mmm) REVERT: A 465 VAL cc_start: 0.7734 (OUTLIER) cc_final: 0.7448 (m) REVERT: A 519 ASP cc_start: 0.7519 (m-30) cc_final: 0.7194 (m-30) REVERT: A 584 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7498 (mp-120) REVERT: A 607 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6974 (mm-30) REVERT: A 742 MET cc_start: 0.5226 (tpp) cc_final: 0.4714 (ptt) REVERT: A 858 ARG cc_start: 0.4920 (OUTLIER) cc_final: 0.4130 (mmp-170) REVERT: B 218 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.5936 (mp) REVERT: B 305 GLU cc_start: 0.5889 (OUTLIER) cc_final: 0.5283 (tm-30) REVERT: B 374 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: B 400 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8190 (m) REVERT: B 465 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7613 (m) REVERT: B 519 ASP cc_start: 0.7544 (m-30) cc_final: 0.7236 (m-30) REVERT: B 587 MET cc_start: 0.9436 (mtp) cc_final: 0.9159 (mtp) REVERT: B 607 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: B 742 MET cc_start: 0.5072 (tpp) cc_final: 0.4640 (ptp) REVERT: B 806 MET cc_start: 0.5042 (tpp) cc_final: 0.4010 (tpt) REVERT: C 304 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6017 (ptm160) REVERT: C 305 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.4923 (tm-30) REVERT: C 374 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: C 415 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7309 (tptm) REVERT: C 421 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.6372 (mpp) REVERT: C 607 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7022 (mm-30) REVERT: C 742 MET cc_start: 0.5031 (tpp) cc_final: 0.4520 (ptp) REVERT: C 806 MET cc_start: 0.5228 (tpp) cc_final: 0.4414 (tpt) outliers start: 78 outliers final: 46 residues processed: 261 average time/residue: 0.6192 time to fit residues: 180.1401 Evaluate side-chains 265 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 198 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 857 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 188 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN B 94 HIS B 512 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.173204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114151 restraints weight = 17722.819| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.71 r_work: 0.3153 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17427 Z= 0.149 Angle : 0.520 8.375 23652 Z= 0.281 Chirality : 0.041 0.147 2598 Planarity : 0.004 0.054 3066 Dihedral : 6.006 56.790 2532 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.99 % Allowed : 18.29 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.18), residues: 2103 helix: 3.13 (0.19), residues: 732 sheet: 0.91 (0.21), residues: 591 loop : -0.24 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 406 TYR 0.010 0.001 TYR B 849 PHE 0.023 0.002 PHE C 793 TRP 0.015 0.002 TRP A 369 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00339 (17409) covalent geometry : angle 0.51858 (23610) SS BOND : bond 0.00530 ( 12) SS BOND : angle 0.91489 ( 24) hydrogen bonds : bond 0.04985 ( 896) hydrogen bonds : angle 4.51780 ( 2670) link_BETA1-4 : bond 0.00128 ( 3) link_BETA1-4 : angle 0.96898 ( 9) link_NAG-ASN : bond 0.00023 ( 3) link_NAG-ASN : angle 1.10701 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 200 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: A 305 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5463 (tm-30) REVERT: A 374 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: A 415 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7298 (tttm) REVERT: A 421 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8226 (mmm) REVERT: A 465 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7480 (m) REVERT: A 584 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7444 (mp-120) REVERT: A 607 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7056 (mm-30) REVERT: A 704 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8232 (mm-30) REVERT: A 742 MET cc_start: 0.5181 (tpp) cc_final: 0.4707 (ptt) REVERT: A 806 MET cc_start: 0.5353 (tpp) cc_final: 0.4248 (tpt) REVERT: A 858 ARG cc_start: 0.4951 (OUTLIER) cc_final: 0.4131 (mmp-170) REVERT: B 304 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6329 (ptm160) REVERT: B 305 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5134 (tm-30) REVERT: B 374 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: B 400 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8205 (m) REVERT: B 465 VAL cc_start: 0.7900 (OUTLIER) cc_final: 0.7661 (m) REVERT: B 519 ASP cc_start: 0.7619 (m-30) cc_final: 0.7340 (m-30) REVERT: B 607 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: B 742 MET cc_start: 0.5063 (tpp) cc_final: 0.4665 (ptp) REVERT: C 304 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6073 (ptm160) REVERT: C 305 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.4999 (tm-30) REVERT: C 374 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: C 415 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7366 (tptm) REVERT: C 465 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7531 (m) REVERT: C 607 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7087 (mm-30) REVERT: C 742 MET cc_start: 0.5078 (tpp) cc_final: 0.4584 (ptp) REVERT: C 856 MET cc_start: 0.6039 (ppp) cc_final: 0.5348 (tpt) outliers start: 89 outliers final: 55 residues processed: 273 average time/residue: 0.6098 time to fit residues: 185.6863 Evaluate side-chains 276 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 199 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 731 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 73 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 512 HIS C 512 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.174160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115611 restraints weight = 17707.203| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.95 r_work: 0.3159 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17427 Z= 0.119 Angle : 0.493 9.272 23652 Z= 0.264 Chirality : 0.039 0.144 2598 Planarity : 0.004 0.054 3066 Dihedral : 5.855 55.955 2532 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.49 % Allowed : 18.63 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.18), residues: 2103 helix: 3.15 (0.19), residues: 732 sheet: 0.91 (0.22), residues: 591 loop : -0.17 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 428 TYR 0.011 0.001 TYR C 849 PHE 0.019 0.001 PHE B 793 TRP 0.019 0.002 TRP A 369 HIS 0.003 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00258 (17409) covalent geometry : angle 0.49184 (23610) SS BOND : bond 0.00409 ( 12) SS BOND : angle 0.76245 ( 24) hydrogen bonds : bond 0.04630 ( 896) hydrogen bonds : angle 4.47398 ( 2670) link_BETA1-4 : bond 0.00235 ( 3) link_BETA1-4 : angle 0.91428 ( 9) link_NAG-ASN : bond 0.00147 ( 3) link_NAG-ASN : angle 1.02800 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 205 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: A 305 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5409 (tm-30) REVERT: A 374 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: A 415 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7274 (tttm) REVERT: A 421 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8179 (mmm) REVERT: A 465 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7479 (m) REVERT: A 519 ASP cc_start: 0.7513 (m-30) cc_final: 0.7288 (m-30) REVERT: A 584 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7481 (mp-120) REVERT: A 607 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6991 (mm-30) REVERT: A 704 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8270 (mm-30) REVERT: A 742 MET cc_start: 0.5104 (tpp) cc_final: 0.4675 (ptt) REVERT: A 806 MET cc_start: 0.5357 (tpp) cc_final: 0.4287 (tpt) REVERT: A 850 MET cc_start: 0.6158 (mmm) cc_final: 0.4837 (mmt) REVERT: A 856 MET cc_start: 0.5903 (ppp) cc_final: 0.5276 (tpt) REVERT: A 858 ARG cc_start: 0.4953 (OUTLIER) cc_final: 0.4121 (mmp-170) REVERT: B 304 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6174 (ptm160) REVERT: B 305 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5042 (tm-30) REVERT: B 374 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: B 400 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8205 (m) REVERT: B 465 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7635 (m) REVERT: B 519 ASP cc_start: 0.7603 (m-30) cc_final: 0.7301 (m-30) REVERT: B 607 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: B 704 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8190 (mm-30) REVERT: B 742 MET cc_start: 0.5017 (tpp) cc_final: 0.4584 (ptp) REVERT: B 806 MET cc_start: 0.5343 (tpp) cc_final: 0.4392 (tpt) REVERT: B 856 MET cc_start: 0.5865 (ppp) cc_final: 0.4924 (mmp) REVERT: C 304 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6044 (ptm160) REVERT: C 305 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.4946 (tm-30) REVERT: C 374 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: C 415 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7359 (tptm) REVERT: C 465 VAL cc_start: 0.7769 (OUTLIER) cc_final: 0.7537 (m) REVERT: C 607 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7062 (mm-30) REVERT: C 742 MET cc_start: 0.5080 (tpp) cc_final: 0.4607 (ptp) REVERT: C 806 MET cc_start: 0.5410 (tpp) cc_final: 0.4594 (tpt) outliers start: 80 outliers final: 53 residues processed: 265 average time/residue: 0.6260 time to fit residues: 184.7212 Evaluate side-chains 280 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 204 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 731 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 144 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN B 512 HIS C 177 HIS C 512 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.173223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114506 restraints weight = 17593.140| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.97 r_work: 0.3140 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17427 Z= 0.146 Angle : 0.524 9.341 23652 Z= 0.281 Chirality : 0.041 0.147 2598 Planarity : 0.004 0.054 3066 Dihedral : 6.002 56.802 2532 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.43 % Allowed : 18.86 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.18), residues: 2103 helix: 3.10 (0.19), residues: 732 sheet: 0.89 (0.22), residues: 591 loop : -0.22 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 428 TYR 0.012 0.001 TYR C 849 PHE 0.024 0.002 PHE C 793 TRP 0.024 0.002 TRP A 369 HIS 0.003 0.001 HIS B 637 Details of bonding type rmsd covalent geometry : bond 0.00329 (17409) covalent geometry : angle 0.52301 (23610) SS BOND : bond 0.00504 ( 12) SS BOND : angle 0.89191 ( 24) hydrogen bonds : bond 0.04967 ( 896) hydrogen bonds : angle 4.52642 ( 2670) link_BETA1-4 : bond 0.00141 ( 3) link_BETA1-4 : angle 0.95900 ( 9) link_NAG-ASN : bond 0.00066 ( 3) link_NAG-ASN : angle 1.07125 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 197 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: A 305 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5431 (tm-30) REVERT: A 374 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: A 415 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7288 (tttm) REVERT: A 421 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8224 (mmm) REVERT: A 465 VAL cc_start: 0.7755 (OUTLIER) cc_final: 0.7478 (m) REVERT: A 519 ASP cc_start: 0.7638 (m-30) cc_final: 0.7366 (m-30) REVERT: A 584 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7496 (mp-120) REVERT: A 607 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7039 (mm-30) REVERT: A 704 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8281 (mm-30) REVERT: A 742 MET cc_start: 0.5121 (tpp) cc_final: 0.4674 (ptt) REVERT: A 806 MET cc_start: 0.5404 (tpp) cc_final: 0.4328 (tpt) REVERT: A 850 MET cc_start: 0.6211 (mmm) cc_final: 0.4768 (mmt) REVERT: A 856 MET cc_start: 0.5898 (ppp) cc_final: 0.4906 (ttp) REVERT: A 858 ARG cc_start: 0.5014 (OUTLIER) cc_final: 0.4160 (mmp-170) REVERT: B 304 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6267 (ptm160) REVERT: B 305 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5129 (tm-30) REVERT: B 374 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: B 400 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8194 (m) REVERT: B 465 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7630 (m) REVERT: B 519 ASP cc_start: 0.7648 (m-30) cc_final: 0.7346 (m-30) REVERT: B 607 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: B 704 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8214 (mm-30) REVERT: B 742 MET cc_start: 0.5005 (tpp) cc_final: 0.4566 (ptp) REVERT: B 806 MET cc_start: 0.5351 (tpp) cc_final: 0.4372 (tpt) REVERT: B 856 MET cc_start: 0.5890 (ppp) cc_final: 0.4976 (mmp) REVERT: C 304 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6064 (ptm160) REVERT: C 305 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.4971 (tm-30) REVERT: C 360 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6368 (mpp-170) REVERT: C 374 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: C 400 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8194 (m) REVERT: C 415 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7331 (tptm) REVERT: C 465 VAL cc_start: 0.7771 (OUTLIER) cc_final: 0.7540 (m) REVERT: C 607 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7040 (mm-30) REVERT: C 742 MET cc_start: 0.5071 (tpp) cc_final: 0.4611 (ptp) REVERT: C 806 MET cc_start: 0.5413 (tpp) cc_final: 0.4744 (tpt) REVERT: C 856 MET cc_start: 0.6007 (ppp) cc_final: 0.5096 (ttp) outliers start: 79 outliers final: 54 residues processed: 259 average time/residue: 0.6343 time to fit residues: 182.7399 Evaluate side-chains 276 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 197 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 731 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 128 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 188 optimal weight: 0.0980 chunk 180 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN B 94 HIS B 512 HIS C 512 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.173809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117885 restraints weight = 17741.931| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.04 r_work: 0.3157 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17427 Z= 0.127 Angle : 0.501 9.287 23652 Z= 0.269 Chirality : 0.040 0.145 2598 Planarity : 0.004 0.054 3066 Dihedral : 5.891 56.202 2532 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.71 % Allowed : 18.46 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.18), residues: 2103 helix: 3.14 (0.19), residues: 732 sheet: 0.90 (0.22), residues: 591 loop : -0.19 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 428 TYR 0.011 0.001 TYR A 849 PHE 0.020 0.001 PHE B 793 TRP 0.024 0.002 TRP A 369 HIS 0.003 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00278 (17409) covalent geometry : angle 0.50011 (23610) SS BOND : bond 0.00433 ( 12) SS BOND : angle 0.79576 ( 24) hydrogen bonds : bond 0.04722 ( 896) hydrogen bonds : angle 4.47916 ( 2670) link_BETA1-4 : bond 0.00216 ( 3) link_BETA1-4 : angle 0.93063 ( 9) link_NAG-ASN : bond 0.00125 ( 3) link_NAG-ASN : angle 1.04820 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9046.91 seconds wall clock time: 154 minutes 7.16 seconds (9247.16 seconds total)