Starting phenix.real_space_refine on Sat Feb 17 02:41:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1c_11983/02_2024/7b1c_11983.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1c_11983/02_2024/7b1c_11983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1c_11983/02_2024/7b1c_11983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1c_11983/02_2024/7b1c_11983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1c_11983/02_2024/7b1c_11983.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1c_11983/02_2024/7b1c_11983.pdb" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 86 5.16 5 C 10788 2.51 5 N 2929 2.21 5 O 3394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17197 Number of models: 1 Model: "" Number of chains: 21 Chain: "C" Number of atoms: 5064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5064 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 271} Link IDs: {'PTRANS': 33, 'TRANS': 716} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 970 Unresolved non-hydrogen angles: 1228 Unresolved non-hydrogen dihedrals: 780 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 27, 'TYR:plan': 3, 'ASN:plan1': 22, 'TRP:plan': 1, 'HIS:plan': 11, 'PHE:plan': 12, 'GLU:plan': 28, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 584 Chain: "A" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 4943 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 318} Link IDs: {'PTRANS': 33, 'TRANS': 718} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1108 Unresolved non-hydrogen angles: 1393 Unresolved non-hydrogen dihedrals: 888 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 19, 'TYR:plan': 3, 'ASN:plan1': 30, 'TRP:plan': 1, 'HIS:plan': 11, 'PHE:plan': 10, 'GLU:plan': 36, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 629 Chain: "D" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 675 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 91} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 513 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 86} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 5530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5530 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 33, 'TRANS': 717} Unresolved non-hydrogen bonds: 488 Unresolved non-hydrogen angles: 611 Unresolved non-hydrogen dihedrals: 388 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 19, 'TYR:plan': 1, 'ASN:plan1': 14, 'HIS:plan': 7, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 339 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: "H" 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: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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: "M" 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: "N" 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" 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: "R" 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.03, per 1000 atoms: 0.58 Number of scatterers: 17197 At special positions: 0 Unit cell: (102.92, 138.61, 198.37, 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 86 16.00 O 3394 8.00 N 2929 7.00 C 10788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 46 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 57 " distance=2.03 Simple disulfide: pdb=" SG CYS C 78 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 559 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 561 " - pdb=" SG CYS C 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 616 " - pdb=" SG CYS C 622 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 767 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 783 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 46 " distance=2.02 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 561 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 616 " - pdb=" SG CYS A 622 " distance=2.02 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 783 " distance=2.03 Simple disulfide: pdb=" SG CYS D 10 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 95 " distance=2.02 Simple disulfide: pdb=" SG CYS D 56 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 59 " - pdb=" SG CYS P 59 " distance=2.02 Simple disulfide: pdb=" SG CYS D 94 " - pdb=" SG CYS P 94 " distance=1.96 Simple disulfide: pdb=" SG CYS P 10 " - pdb=" SG CYS P 65 " distance=2.03 Simple disulfide: pdb=" SG CYS P 47 " - pdb=" SG CYS P 95 " distance=2.02 Simple disulfide: pdb=" SG CYS P 56 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 57 " distance=2.04 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 561 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 622 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 767 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 783 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 801 " - " ASN A 687 " " NAG B 801 " - " ASN B 525 " " NAG C 801 " - " ASN C 521 " " NAG E 1 " - " ASN C 151 " " NAG F 1 " - " ASN B 634 " " NAG G 1 " - " ASN C 194 " " NAG H 1 " - " ASN C 481 " " NAG I 1 " - " ASN A 521 " " NAG J 1 " - " ASN A 194 " " NAG K 1 " - " ASN A 151 " " NAG L 1 " - " ASN A 481 " " NAG M 1 " - " ASN A 634 " " NAG N 1 " - " ASN B 481 " " NAG O 1 " - " ASN B 521 " " NAG Q 1 " - " ASN B 194 " " NAG R 1 " - " ASN B 151 " Time building additional restraints: 8.04 Conformation dependent library (CDL) restraints added in 3.6 seconds 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4728 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 29 sheets defined 14.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 117 through 120 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.660A pdb=" N GLY C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.813A pdb=" N LEU C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 4.041A pdb=" N PHE C 237 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN C 238 " --> pdb=" O GLY C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.099A pdb=" N LYS C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 463 removed outlier: 3.624A pdb=" N ASP C 462 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN C 463 " --> pdb=" O ILE C 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 459 through 463' Processing helix chain 'C' and resid 466 through 471 removed outlier: 3.946A pdb=" N VAL C 470 " --> pdb=" O THR C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 494 Processing helix chain 'C' and resid 514 through 517 Processing helix chain 'C' and resid 560 through 571 Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.740A pdb=" N GLY C 637 " --> pdb=" O ASN C 634 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG C 638 " --> pdb=" O CYS C 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 634 through 638' Processing helix chain 'C' and resid 653 through 658 Processing helix chain 'C' and resid 716 through 723 Processing helix chain 'C' and resid 742 through 751 Processing helix chain 'C' and resid 752 through 762 removed outlier: 3.928A pdb=" N ARG C 757 " --> pdb=" O GLN C 753 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 778 Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.283A pdb=" N SER A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 257 through 263 removed outlier: 3.661A pdb=" N PHE A 261 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 263 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 4.041A pdb=" N ASN A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.363A pdb=" N LEU A 334 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 removed outlier: 4.546A pdb=" N LEU A 382 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 4.070A pdb=" N PHE A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 removed outlier: 3.515A pdb=" N VAL A 470 " --> pdb=" O PRO A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 716 through 723 removed outlier: 4.212A pdb=" N LEU A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 773 through 777 Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'P' and resid 49 through 52 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 139 through 144 removed outlier: 3.582A pdb=" N TYR B 142 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 4.314A pdb=" N GLY B 168 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 4.186A pdb=" N PHE B 237 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.785A pdb=" N PHE B 406 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 514 through 517 Processing helix chain 'B' and resid 563 through 571 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 650 through 655 removed outlier: 3.538A pdb=" N ASP B 655 " --> pdb=" O GLN B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 724 removed outlier: 3.925A pdb=" N GLN B 722 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 724 " --> pdb=" O ALA B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 755 removed outlier: 3.835A pdb=" N PHE B 748 " --> pdb=" O PRO B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 759 Processing helix chain 'B' and resid 773 through 777 Processing helix chain 'B' and resid 780 through 784 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 47 removed outlier: 5.969A pdb=" N VAL C 74 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL C 102 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE C 76 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 152 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 175 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 200 through 201 removed outlier: 6.988A pdb=" N LEU C 246 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR C 273 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU C 248 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 297 " --> pdb=" O ILE C 272 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 438 through 440 removed outlier: 7.585A pdb=" N ILE C 439 " --> pdb=" O HIS C 478 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU C 477 " --> pdb=" O ASP C 502 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C 501 " --> pdb=" O ASN C 525 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C 548 " --> pdb=" O GLN C 579 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASN C 581 " --> pdb=" O ILE C 548 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 550 " --> pdb=" O ASN C 581 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 510 through 512 removed outlier: 6.764A pdb=" N LEU C 511 " --> pdb=" O LEU C 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 586 through 587 Processing sheet with id=AA6, first strand: chain 'C' and resid 766 through 767 Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA8, first strand: chain 'A' and resid 64 through 68 removed outlier: 8.147A pdb=" N VAL A 102 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE A 76 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL A 101 " --> pdb=" O ASN A 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 138 removed outlier: 6.502A pdb=" N ILE A 136 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A 160 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 174 through 178 removed outlier: 3.617A pdb=" N VAL A 201 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 246 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N THR A 273 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 248 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 297 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 343 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 368 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 367 " --> pdb=" O TYR A 392 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 438 through 439 removed outlier: 5.953A pdb=" N ILE A 439 " --> pdb=" O HIS A 478 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 502 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 501 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 551 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE A 548 " --> pdb=" O GLN A 579 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 447 through 448 removed outlier: 3.897A pdb=" N LEU A 448 " --> pdb=" O SER A 483 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 511 through 512 removed outlier: 6.301A pdb=" N LEU A 511 " --> pdb=" O LEU A 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 623 through 625 removed outlier: 3.573A pdb=" N THR A 630 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 659 " --> pdb=" O GLN A 682 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 704 through 708 removed outlier: 3.744A pdb=" N SER A 735 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 12 through 17 Processing sheet with id=AB9, first strand: chain 'D' and resid 85 through 99 removed outlier: 5.244A pdb=" N LYS D 86 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ALA D 76 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN D 88 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU D 74 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU D 90 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ARG D 72 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N HIS D 70 " --> pdb=" O PRO D 92 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 98 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 20.206A pdb=" N GLN D 67 " --> pdb=" O CYS P 47 " (cutoff:3.500A) removed outlier: 17.137A pdb=" N CYS P 47 " --> pdb=" O GLN D 67 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N PHE D 69 " --> pdb=" O GLU P 45 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N GLU P 45 " --> pdb=" O PHE D 69 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR D 71 " --> pdb=" O ARG P 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 66 through 73 removed outlier: 6.416A pdb=" N LYS P 66 " --> pdb=" O CYS P 95 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS P 95 " --> pdb=" O LYS P 66 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU P 68 " --> pdb=" O SER P 93 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER P 93 " --> pdb=" O LEU P 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.554A pdb=" N ASP B 67 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 74 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N VAL B 102 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE B 76 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 128 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE B 127 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA B 155 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR B 129 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 176 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU B 198 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU B 246 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N THR B 273 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 248 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 94 through 95 removed outlier: 7.078A pdb=" N GLY B 94 " --> pdb=" O ALA B 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AC5, first strand: chain 'B' and resid 390 through 392 removed outlier: 3.652A pdb=" N LEU B 391 " --> pdb=" O GLU B 414 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 415 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 500 through 502 Processing sheet with id=AC7, first strand: chain 'B' and resid 511 through 512 removed outlier: 7.155A pdb=" N LEU B 511 " --> pdb=" O LEU B 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 556 through 557 removed outlier: 6.429A pdb=" N ARG B 586 " --> pdb=" O LEU B 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 623 through 625 Processing sheet with id=AD1, first strand: chain 'B' and resid 682 through 683 Processing sheet with id=AD2, first strand: chain 'B' and resid 738 through 739 278 hydrogen bonds defined for protein. 657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 8.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5251 1.34 - 1.47: 3697 1.47 - 1.60: 8406 1.60 - 1.72: 0 1.72 - 1.85: 103 Bond restraints: 17457 Sorted by residual: bond pdb=" N ILE B 425 " pdb=" CA ILE B 425 " ideal model delta sigma weight residual 1.461 1.495 -0.034 8.70e-03 1.32e+04 1.51e+01 bond pdb=" N ILE C 341 " pdb=" CA ILE C 341 " ideal model delta sigma weight residual 1.460 1.493 -0.033 8.60e-03 1.35e+04 1.48e+01 bond pdb=" N ILE B 698 " pdb=" CA ILE B 698 " ideal model delta sigma weight residual 1.461 1.496 -0.035 9.10e-03 1.21e+04 1.47e+01 bond pdb=" N ILE B 454 " pdb=" CA ILE B 454 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.04e-02 9.25e+03 1.43e+01 bond pdb=" N THR B 466 " pdb=" CA THR B 466 " ideal model delta sigma weight residual 1.453 1.486 -0.033 9.20e-03 1.18e+04 1.30e+01 ... (remaining 17452 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.65: 376 105.65 - 112.73: 9534 112.73 - 119.81: 6129 119.81 - 126.89: 7786 126.89 - 133.97: 115 Bond angle restraints: 23940 Sorted by residual: angle pdb=" N LEU C 198 " pdb=" CA LEU C 198 " pdb=" C LEU C 198 " ideal model delta sigma weight residual 113.20 102.90 10.30 1.21e+00 6.83e-01 7.25e+01 angle pdb=" N ILE C 341 " pdb=" CA ILE C 341 " pdb=" C ILE C 341 " ideal model delta sigma weight residual 113.71 107.32 6.39 9.50e-01 1.11e+00 4.52e+01 angle pdb=" N VAL A 74 " pdb=" CA VAL A 74 " pdb=" C VAL A 74 " ideal model delta sigma weight residual 108.35 99.91 8.44 1.32e+00 5.74e-01 4.09e+01 angle pdb=" N GLN A 472 " pdb=" CA GLN A 472 " pdb=" C GLN A 472 " ideal model delta sigma weight residual 114.56 106.60 7.96 1.27e+00 6.20e-01 3.93e+01 angle pdb=" N PHE C 60 " pdb=" CA PHE C 60 " pdb=" C PHE C 60 " ideal model delta sigma weight residual 113.18 105.33 7.85 1.33e+00 5.65e-01 3.48e+01 ... (remaining 23935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 10433 21.92 - 43.84: 477 43.84 - 65.76: 108 65.76 - 87.68: 49 87.68 - 109.60: 25 Dihedral angle restraints: 11092 sinusoidal: 3882 harmonic: 7210 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 104 " pdb=" CB CYS A 104 " ideal model delta sinusoidal sigma weight residual 93.00 -178.93 -88.07 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 783 " pdb=" CB CYS B 783 " ideal model delta sinusoidal sigma weight residual -86.00 -171.28 85.28 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS C 561 " pdb=" SG CYS C 561 " pdb=" SG CYS C 608 " pdb=" CB CYS C 608 " ideal model delta sinusoidal sigma weight residual -86.00 -171.10 85.10 1 1.00e+01 1.00e-02 8.78e+01 ... (remaining 11089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2644 0.110 - 0.220: 372 0.220 - 0.330: 44 0.330 - 0.440: 1 0.440 - 0.551: 1 Chirality restraints: 3062 Sorted by residual: chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.95 0.55 2.00e-02 2.50e+03 7.58e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.25e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 9.69e+00 ... (remaining 3059 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.283 2.00e-02 2.50e+03 2.44e-01 7.44e+02 pdb=" C7 NAG N 1 " -0.061 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.010 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.415 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.071 2.00e-02 2.50e+03 5.90e-02 4.34e+01 pdb=" C7 NAG N 2 " 0.020 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.054 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.094 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.048 2.00e-02 2.50e+03 3.92e-02 1.93e+01 pdb=" C7 NAG L 1 " 0.014 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.062 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.008 2.00e-02 2.50e+03 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 701 2.69 - 3.24: 18665 3.24 - 3.80: 27183 3.80 - 4.35: 35673 4.35 - 4.90: 55971 Nonbonded interactions: 138193 Sorted by model distance: nonbonded pdb=" OD1 ASP B 75 " pdb=" N PHE B 76 " model vdw 2.139 2.520 nonbonded pdb=" OD1 ASP A 109 " pdb=" NH1 ARG A 110 " model vdw 2.149 2.520 nonbonded pdb=" OG SER B 726 " pdb=" O HIS B 728 " model vdw 2.218 2.440 nonbonded pdb=" O ASP A 716 " pdb=" OG1 THR A 719 " model vdw 2.219 2.440 nonbonded pdb=" O THR C 597 " pdb=" N LEU C 601 " model vdw 2.233 2.520 ... (remaining 138188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 36 or (resid 37 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 46 or (resid 47 through \ 48 and (name N or name CA or name C or name O or name CB )) or resid 49 through \ 50 or (resid 51 through 53 and (name N or name CA or name C or name O or name C \ B )) or resid 54 through 58 or (resid 59 through 61 and (name N or name CA or na \ me C or name O or name CB )) or resid 62 through 68 or (resid 69 through 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 through 79 or ( \ resid 80 through 81 and (name N or name CA or name C or name O or name CB )) or \ resid 82 through 83 or (resid 84 and (name N or name CA or name C or name O or n \ ame CB )) or resid 85 through 86 or (resid 87 through 88 and (name N or name CA \ or name C or name O or name CB )) or resid 89 through 94 or (resid 95 through 98 \ and (name N or name CA or name C or name O or name CB )) or resid 99 through 10 \ 2 or (resid 103 and (name N or name CA or name C or name O or name CB )) or resi \ d 104 through 118 or (resid 119 through 123 and (name N or name CA or name C or \ name O or name CB )) or resid 124 through 131 or (resid 132 through 134 and (nam \ e N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thro \ ugh 138 and (name N or name CA or name C or name O or name CB )) or resid 139 th \ rough 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) \ or resid 142 or (resid 143 through 144 and (name N or name CA or name C or name \ O or name CB )) or (resid 145 through 147 and (name N or name CA or name C or n \ ame O or name CB )) or resid 148 through 158 or (resid 159 and (name N or name C \ A or name C or name O or name CB )) or resid 160 or (resid 161 through 166 and ( \ name N or name CA or name C or name O or name CB )) or resid 167 through 168 or \ (resid 169 and (name N or name CA or name C or name O or name CB )) or resid 170 \ through 181 or (resid 182 and (name N or name CA or name C or name O or name CB \ )) or resid 183 through 184 or (resid 185 and (name N or name CA or name C or n \ ame O or name CB )) or resid 186 through 187 or (resid 188 and (name N or name C \ A or name C or name O or name CB )) or resid 189 through 191 or (resid 192 and ( \ name N or name CA or name C or name O or name CB )) or resid 193 through 194 or \ (resid 195 through 198 and (name N or name CA or name C or name O or name CB )) \ or resid 199 through 201 or (resid 202 through 203 and (name N or name CA or nam \ e C or name O or name CB )) or resid 204 through 223 or (resid 224 and (name N o \ r name CA or name C or name O or name CB )) or resid 225 through 250 or (resid 2 \ 51 through 252 and (name N or name CA or name C or name O or name CB )) or resid \ 253 through 272 or (resid 273 and (name N or name CA or name C or name O or nam \ e CB )) or resid 274 or (resid 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 292 or (resid 293 and (name N or name CA or nam \ e C or name O or name CB )) or resid 294 or (resid 295 through 324 and (name N o \ r name CA or name C or name O or name CB )) or resid 325 through 448 or (resid 4 \ 49 through 480 and (name N or name CA or name C or name O or name CB )) or resid \ 481 through 489 or (resid 490 and (name N or name CA or name C or name O or nam \ e CB )) or resid 491 through 495 or (resid 496 through 497 and (name N or name C \ A or name C or name O or name CB )) or resid 498 through 507 or (resid 508 and ( \ name N or name CA or name C or name O or name CB )) or resid 509 through 537 or \ (resid 538 through 539 and (name N or name CA or name C or name O or name CB )) \ or resid 540 or (resid 541 through 543 and (name N or name CA or name C or name \ O or name CB )) or resid 544 through 561 or (resid 562 through 563 and (name N o \ r name CA or name C or name O or name CB )) or resid 564 or (resid 565 and (name \ N or name CA or name C or name O or name CB )) or resid 566 or (resid 567 throu \ gh 569 and (name N or name CA or name C or name O or name CB )) or resid 570 or \ (resid 571 through 576 and (name N or name CA or name C or name O or name CB )) \ or resid 577 through 580 or (resid 581 and (name N or name CA or name C or name \ O or name CB )) or resid 582 or (resid 583 through 584 and (name N or name CA or \ name C or name O or name CB )) or resid 585 or (resid 586 and (name N or name C \ A or name C or name O or name CB )) or resid 587 or (resid 588 and (name N or na \ me CA or name C or name O or name CB )) or resid 589 through 591 or (resid 592 t \ hrough 594 and (name N or name CA or name C or name O or name CB )) or resid 595 \ through 596 or (resid 597 and (name N or name CA or name C or name O or name CB \ )) or resid 598 or (resid 599 through 606 and (name N or name CA or name C or n \ ame O or name CB )) or resid 607 through 608 or (resid 609 through 615 and (name \ N or name CA or name C or name O or name CB )) or resid 616 through 618 or (res \ id 619 and (name N or name CA or name C or name O or name CB )) or resid 620 thr \ ough 625 or (resid 626 through 636 and (name N or name CA or name C or name O or \ name CB )) or (resid 637 through 740 and (name N or name CA or name C or name O \ or name CB )) or resid 741 through 774 or (resid 775 through 776 and (name N or \ name CA or name C or name O or name CB )) or resid 777 or (resid 778 through 78 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 783 or resid \ 801)) selection = (chain 'B' and (resid 35 through 50 or (resid 51 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 62 or (resid 63 and (na \ me N or name CA or name C or name O or name CB )) or resid 64 through 72 or (res \ id 73 and (name N or name CA or name C or name O or name CB )) or resid 74 or (r \ esid 75 and (name N or name CA or name C or name O or name CB )) or resid 76 or \ (resid 77 and (name N or name CA or name C or name O or name CB )) or resid 78 t \ hrough 86 or (resid 87 through 88 and (name N or name CA or name C or name O or \ name CB )) or resid 89 through 94 or (resid 95 through 98 and (name N or name CA \ or name C or name O or name CB )) or resid 99 through 102 or (resid 103 and (na \ me N or name CA or name C or name O or name CB )) or resid 104 through 118 or (r \ esid 119 through 123 and (name N or name CA or name C or name O or name CB )) or \ resid 124 through 131 or (resid 132 through 134 and (name N or name CA or name \ C or name O or name CB )) or resid 135 or (resid 136 through 138 and (name N or \ name CA or name C or name O or name CB )) or resid 139 through 140 or (resid 141 \ and (name N or name CA or name C or name O or name CB )) or resid 142 or (resid \ 143 through 144 and (name N or name CA or name C or name O or name CB )) or res \ id 145 or (resid 146 through 147 and (name N or name CA or name C or name O or n \ ame CB )) or resid 148 through 158 or (resid 159 and (name N or name CA or name \ C or name O or name CB )) or resid 160 or (resid 161 through 166 and (name N or \ name CA or name C or name O or name CB )) or resid 167 through 168 or (resid 169 \ and (name N or name CA or name C or name O or name CB )) or resid 170 or (resid \ 171 through 173 and (name N or name CA or name C or name O or name CB )) or res \ id 174 through 177 or (resid 178 and (name N or name CA or name C or name O or n \ ame CB )) or resid 179 through 180 or (resid 181 through 182 and (name N or name \ CA or name C or name O or name CB )) or resid 183 through 187 or (resid 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 191 o \ r (resid 192 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 93 through 194 or (resid 195 through 198 and (name N or name CA or name C or nam \ e O or name CB )) or resid 199 through 205 or (resid 206 through 209 and (name N \ or name CA or name C or name O or name CB )) or resid 210 through 211 or (resid \ 212 through 214 and (name N or name CA or name C or name O or name CB )) or res \ id 215 through 216 or (resid 217 through 218 and (name N or name CA or name C or \ name O or name CB )) or resid 219 or (resid 220 through 221 and (name N or name \ CA or name C or name O or name CB )) or resid 222 through 227 or (resid 228 and \ (name N or name CA or name C or name O or name CB )) or resid 229 or (resid 230 \ and (name N or name CA or name C or name O or name CB )) or resid 231 through 2 \ 32 or (resid 233 through 234 and (name N or name CA or name C or name O or name \ CB )) or resid 235 or (resid 236 and (name N or name CA or name C or name O or n \ ame CB )) or resid 237 or (resid 238 and (name N or name CA or name C or name O \ or name CB )) or resid 239 or (resid 240 through 245 and (name N or name CA or n \ ame C or name O or name CB )) or resid 246 through 248 or (resid 249 and (name N \ or name CA or name C or name O or name CB )) or resid 250 or (resid 251 through \ 252 and (name N or name CA or name C or name O or name CB )) or resid 253 or (r \ esid 254 through 255 and (name N or name CA or name C or name O or name CB )) or \ resid 256 or (resid 257 through 259 and (name N or name CA or name C or name O \ or name CB )) or resid 260 through 264 or (resid 265 through 266 and (name N or \ name CA or name C or name O or name CB )) or resid 267 through 268 or (resid 269 \ and (name N or name CA or name C or name O or name CB )) or resid 270 through 2 \ 72 or (resid 273 and (name N or name CA or name C or name O or name CB )) or res \ id 274 through 278 or (resid 279 and (name N or name CA or name C or name O or n \ ame CB )) or resid 280 through 281 or (resid 282 and (name N or name CA or name \ C or name O or name CB )) or resid 283 through 285 or (resid 286 through 288 and \ (name N or name CA or name C or name O or name CB )) or resid 289 or (resid 290 \ and (name N or name CA or name C or name O or name CB )) or resid 291 through 2 \ 92 or (resid 293 and (name N or name CA or name C or name O or name CB )) or res \ id 294 through 295 or (resid 296 through 324 and (name N or name CA or name C or \ name O or name CB )) or resid 325 or (resid 326 and (name N or name CA or name \ C or name O or name CB )) or resid 327 or (resid 328 through 335 and (name N or \ name CA or name C or name O or name CB )) or resid 336 or (resid 337 through 338 \ and (name N or name CA or name C or name O or name CB )) or resid 339 or (resid \ 340 through 345 and (name N or name CA or name C or name O or name CB )) or res \ id 346 or (resid 347 through 431 and (name N or name CA or name C or name O or n \ ame CB )) or resid 432 or (resid 433 and (name N or name CA or name C or name O \ or name CB )) or resid 434 or (resid 435 and (name N or name CA or name C or nam \ e O or name CB )) or resid 436 or (resid 437 and (name N or name CA or name C or \ name O or name CB )) or resid 438 through 448 or (resid 449 through 480 and (na \ me N or name CA or name C or name O or name CB )) or resid 481 or (resid 482 thr \ ough 486 and (name N or name CA or name C or name O or name CB )) or resid 487 t \ hrough 489 or (resid 490 and (name N or name CA or name C or name O or name CB ) \ ) or resid 491 through 496 or (resid 497 and (name N or name CA or name C or nam \ e O or name CB )) or resid 498 through 541 or (resid 542 through 543 and (name N \ or name CA or name C or name O or name CB )) or resid 544 through 567 or (resid \ 568 through 569 and (name N or name CA or name C or name O or name CB )) or res \ id 570 through 598 or (resid 599 through 606 and (name N or name CA or name C or \ name O or name CB )) or resid 607 through 609 or (resid 610 through 615 and (na \ me N or name CA or name C or name O or name CB )) or resid 616 through 624 or (r \ esid 625 through 636 and (name N or name CA or name C or name O or name CB )) or \ (resid 637 through 740 and (name N or name CA or name C or name O or name CB )) \ or resid 741 or (resid 742 and (name N or name CA or name C or name O or name C \ B )) or resid 743 through 745 or (resid 746 through 766 and (name N or name CA o \ r name C or name O or name CB )) or resid 767 through 769 or (resid 770 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 771 through 776 and ( \ name N or name CA or name C or name O or name CB )) or resid 777 or (resid 778 t \ hrough 782 and (name N or name CA or name C or name O or name CB )) or resid 783 \ or resid 801)) selection = (chain 'C' and (resid 35 through 37 or (resid 38 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 46 or (resid 47 through \ 48 and (name N or name CA or name C or name O or name CB )) or resid 49 through \ 52 or (resid 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 58 or (resid 59 through 61 and (name N or name CA or name C or nam \ e O or name CB )) or resid 62 or (resid 63 and (name N or name CA or name C or n \ ame O or name CB )) or resid 64 through 74 or (resid 75 and (name N or name CA o \ r name C or name O or name CB )) or resid 76 or (resid 77 and (name N or name CA \ or name C or name O or name CB )) or resid 78 through 95 or (resid 96 through 9 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 99 through 1 \ 70 or (resid 171 through 173 and (name N or name CA or name C or name O or name \ CB )) or resid 174 through 177 or (resid 178 and (name N or name CA or name C or \ name O or name CB )) or resid 179 through 184 or (resid 185 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 201 or (resid 202 thr \ ough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 t \ hrough 205 or (resid 206 through 209 and (name N or name CA or name C or name O \ or name CB )) or resid 210 through 211 or (resid 212 through 214 and (name N or \ name CA or name C or name O or name CB )) or resid 215 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 or (resid \ 220 through 221 and (name N or name CA or name C or name O or name CB )) or res \ id 222 through 232 or (resid 233 through 234 and (name N or name CA or name C or \ name O or name CB )) or resid 235 or (resid 236 and (name N or name CA or name \ C or name O or name CB )) or resid 237 or (resid 238 and (name N or name CA or n \ ame C or name O or name CB )) or resid 239 or (resid 240 through 245 and (name N \ or name CA or name C or name O or name CB )) or resid 246 through 248 or (resid \ 249 and (name N or name CA or name C or name O or name CB )) or resid 250 throu \ gh 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) or \ resid 256 or (resid 257 through 259 and (name N or name CA or name C or name O \ or name CB )) or resid 260 through 264 or (resid 265 through 266 and (name N or \ name CA or name C or name O or name CB )) or resid 267 through 268 or (resid 269 \ and (name N or name CA or name C or name O or name CB )) or resid 270 through 2 \ 74 or (resid 275 and (name N or name CA or name C or name O or name CB )) or res \ id 276 through 278 or (resid 279 and (name N or name CA or name C or name O or n \ ame CB )) or resid 280 through 285 or (resid 286 through 288 and (name N or name \ CA or name C or name O or name CB )) or resid 289 or (resid 290 and (name N or \ name CA or name C or name O or name CB )) or resid 291 through 294 or (resid 295 \ through 324 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 25 or (resid 326 and (name N or name CA or name C or name O or name CB )) or res \ id 327 or (resid 328 through 335 and (name N or name CA or name C or name O or n \ ame CB )) or resid 336 or (resid 337 through 338 and (name N or name CA or name \ C or name O or name CB )) or resid 339 or (resid 340 through 345 and (name N or \ name CA or name C or name O or name CB )) or resid 346 or (resid 347 through 431 \ and (name N or name CA or name C or name O or name CB )) or resid 432 or (resid \ 433 and (name N or name CA or name C or name O or name CB )) or resid 434 or (r \ esid 435 and (name N or name CA or name C or name O or name CB )) or resid 436 o \ r (resid 437 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 38 through 464 or (resid 465 through 480 and (name N or name CA or name C or nam \ e O or name CB )) or resid 481 or (resid 482 through 486 and (name N or name CA \ or name C or name O or name CB )) or resid 487 through 495 or (resid 496 through \ 497 and (name N or name CA or name C or name O or name CB )) or resid 498 throu \ gh 507 or (resid 508 and (name N or name CA or name C or name O or name CB )) or \ resid 509 through 561 or (resid 562 through 563 and (name N or name CA or name \ C or name O or name CB )) or resid 564 or (resid 565 and (name N or name CA or n \ ame C or name O or name CB )) or resid 566 or (resid 567 through 569 and (name N \ or name CA or name C or name O or name CB )) or resid 570 or (resid 571 through \ 576 and (name N or name CA or name C or name O or name CB )) or resid 577 throu \ gh 580 or (resid 581 and (name N or name CA or name C or name O or name CB )) or \ resid 582 or (resid 583 through 584 and (name N or name CA or name C or name O \ or name CB )) or resid 585 or (resid 586 and (name N or name CA or name C or nam \ e O or name CB )) or resid 587 or (resid 588 and (name N or name CA or name C or \ name O or name CB )) or resid 589 through 591 or (resid 592 through 594 and (na \ me N or name CA or name C or name O or name CB )) or resid 595 through 596 or (r \ esid 597 and (name N or name CA or name C or name O or name CB )) or resid 598 t \ hrough 600 or (resid 601 through 606 and (name N or name CA or name C or name O \ or name CB )) or resid 607 through 618 or (resid 619 and (name N or name CA or n \ ame C or name O or name CB )) or resid 620 through 783 or resid 801)) } ncs_group { reference = (chain 'D' and (resid 7 through 19 or (resid 20 through 40 and (name N or name C \ A or name C or name O or name CB )) or resid 41 or (resid 42 through 46 and (nam \ e N or name CA or name C or name O or name CB )) or resid 47 through 54 or (resi \ d 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throug \ h 57 or (resid 58 and (name N or name CA or name C or name O or name CB )) or re \ sid 59 through 62 or (resid 63 through 64 and (name N or name CA or name C or na \ me O or name CB )) or resid 65 or (resid 66 through 83 and (name N or name CA or \ name C or name O or name CB )) or resid 84 or (resid 85 through 89 and (name N \ or name CA or name C or name O or name CB )) or resid 90 through 92 or (resid 93 \ and (name N or name CA or name C or name O or name CB )) or resid 94 through 97 \ )) selection = (chain 'P' and (resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 97)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 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: 12.360 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 50.740 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.010 0.071 17457 Z= 0.657 Angle : 1.233 11.421 23940 Z= 0.833 Chirality : 0.076 0.551 3062 Planarity : 0.007 0.244 3139 Dihedral : 15.531 109.601 6262 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.17 % Allowed : 4.01 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.16), residues: 2430 helix: -1.34 (0.35), residues: 202 sheet: -2.26 (0.25), residues: 415 loop : -1.43 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 491 HIS 0.006 0.001 HIS C 416 PHE 0.016 0.002 PHE A 143 TYR 0.015 0.002 TYR C 440 ARG 0.005 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 2.487 Fit side-chains revert: symmetry clash REVERT: C 189 PHE cc_start: 0.8216 (m-80) cc_final: 0.7852 (m-10) REVERT: C 294 LEU cc_start: 0.9167 (tp) cc_final: 0.8787 (tp) REVERT: B 245 MET cc_start: 0.7914 (tmm) cc_final: 0.6446 (tmm) outliers start: 32 outliers final: 8 residues processed: 102 average time/residue: 0.2751 time to fit residues: 46.4968 Evaluate side-chains 46 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 506 ASN Chi-restraints excluded: chain B residue 551 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 102 optimal weight: 30.0000 chunk 62 optimal weight: 50.0000 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN B 427 GLN B 444 ASN B 682 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17457 Z= 0.264 Angle : 0.686 8.538 23940 Z= 0.341 Chirality : 0.046 0.307 3062 Planarity : 0.004 0.039 3139 Dihedral : 10.241 65.243 3258 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.29 % Allowed : 8.76 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.17), residues: 2430 helix: -1.17 (0.34), residues: 217 sheet: -2.04 (0.24), residues: 446 loop : -1.21 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 491 HIS 0.003 0.001 HIS C 416 PHE 0.016 0.001 PHE C 285 TYR 0.015 0.001 TYR C 440 ARG 0.006 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 37 time to evaluate : 2.271 Fit side-chains REVERT: C 245 MET cc_start: 0.7652 (tpp) cc_final: 0.7272 (tpp) REVERT: C 285 PHE cc_start: 0.9093 (m-80) cc_final: 0.8701 (m-10) REVERT: A 442 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8856 (mp10) REVERT: B 146 MET cc_start: 0.8660 (tpp) cc_final: 0.8344 (mmm) REVERT: B 245 MET cc_start: 0.7895 (tmm) cc_final: 0.7451 (tmm) outliers start: 19 outliers final: 8 residues processed: 56 average time/residue: 0.2543 time to fit residues: 25.3215 Evaluate side-chains 43 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 484 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 183 optimal weight: 30.0000 chunk 150 optimal weight: 20.0000 chunk 60 optimal weight: 50.0000 chunk 221 optimal weight: 8.9990 chunk 238 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 17457 Z= 0.464 Angle : 0.812 9.707 23940 Z= 0.405 Chirality : 0.048 0.298 3062 Planarity : 0.005 0.049 3139 Dihedral : 8.455 57.317 3251 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 2.17 % Allowed : 12.36 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.16), residues: 2430 helix: -1.36 (0.33), residues: 231 sheet: -2.24 (0.24), residues: 420 loop : -1.54 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 491 HIS 0.006 0.001 HIS C 416 PHE 0.020 0.002 PHE C 55 TYR 0.026 0.003 TYR A 226 ARG 0.005 0.001 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 35 time to evaluate : 2.089 Fit side-chains revert: symmetry clash REVERT: C 294 LEU cc_start: 0.9000 (tp) cc_final: 0.8762 (tt) REVERT: B 146 MET cc_start: 0.8912 (tpp) cc_final: 0.8323 (mmm) REVERT: B 245 MET cc_start: 0.7856 (tmm) cc_final: 0.7279 (tmm) REVERT: B 762 MET cc_start: 0.6883 (mmt) cc_final: 0.6412 (mmt) outliers start: 32 outliers final: 18 residues processed: 67 average time/residue: 0.2233 time to fit residues: 27.3861 Evaluate side-chains 51 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 33 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 548 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 114 optimal weight: 40.0000 chunk 24 optimal weight: 10.0000 chunk 105 optimal weight: 50.0000 chunk 148 optimal weight: 40.0000 chunk 221 optimal weight: 0.8980 chunk 234 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 63 optimal weight: 50.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17457 Z= 0.196 Angle : 0.607 8.860 23940 Z= 0.304 Chirality : 0.044 0.313 3062 Planarity : 0.003 0.033 3139 Dihedral : 7.503 59.515 3249 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.29 % Allowed : 14.20 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.17), residues: 2430 helix: -0.88 (0.35), residues: 224 sheet: -2.09 (0.23), residues: 438 loop : -1.27 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 491 HIS 0.003 0.001 HIS C 416 PHE 0.011 0.001 PHE B 49 TYR 0.011 0.001 TYR B 79 ARG 0.004 0.000 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 34 time to evaluate : 2.125 Fit side-chains REVERT: B 146 MET cc_start: 0.8920 (tpp) cc_final: 0.8388 (mmm) REVERT: B 245 MET cc_start: 0.7809 (tmm) cc_final: 0.7228 (tmm) REVERT: B 762 MET cc_start: 0.6736 (mmt) cc_final: 0.6222 (mmt) outliers start: 19 outliers final: 10 residues processed: 53 average time/residue: 0.2197 time to fit residues: 22.4703 Evaluate side-chains 43 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 469 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 174 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 50.0000 chunk 210 optimal weight: 9.9990 chunk 59 optimal weight: 30.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17457 Z= 0.265 Angle : 0.612 8.365 23940 Z= 0.305 Chirality : 0.043 0.318 3062 Planarity : 0.003 0.033 3139 Dihedral : 7.240 59.898 3249 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.04 % Allowed : 14.54 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.17), residues: 2430 helix: -0.85 (0.35), residues: 225 sheet: -1.97 (0.24), residues: 441 loop : -1.26 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 31 HIS 0.003 0.001 HIS C 416 PHE 0.010 0.001 PHE A 55 TYR 0.014 0.001 TYR A 79 ARG 0.004 0.000 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 33 time to evaluate : 2.128 Fit side-chains revert: symmetry clash REVERT: C 219 LEU cc_start: 0.8440 (mt) cc_final: 0.8231 (mt) REVERT: B 146 MET cc_start: 0.8913 (tpp) cc_final: 0.8364 (mmm) REVERT: B 245 MET cc_start: 0.7832 (tmm) cc_final: 0.7217 (tmm) REVERT: B 762 MET cc_start: 0.6736 (mmt) cc_final: 0.6338 (mmt) outliers start: 30 outliers final: 17 residues processed: 63 average time/residue: 0.2094 time to fit residues: 24.9590 Evaluate side-chains 50 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 33 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 469 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 9.9990 chunk 211 optimal weight: 0.1980 chunk 46 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 chunk 195 optimal weight: 0.7980 chunk 108 optimal weight: 50.0000 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 ASN ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17457 Z= 0.238 Angle : 0.600 8.736 23940 Z= 0.298 Chirality : 0.043 0.319 3062 Planarity : 0.003 0.034 3139 Dihedral : 7.047 59.569 3249 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.90 % Allowed : 15.08 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2430 helix: -0.66 (0.36), residues: 219 sheet: -1.96 (0.24), residues: 422 loop : -1.21 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 491 HIS 0.002 0.001 HIS C 416 PHE 0.009 0.001 PHE D 58 TYR 0.013 0.001 TYR A 79 ARG 0.002 0.000 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 33 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 219 LEU cc_start: 0.8463 (mt) cc_final: 0.8243 (mt) REVERT: C 624 MET cc_start: 0.2078 (tpp) cc_final: 0.1597 (tpp) REVERT: A 441 MET cc_start: 0.8326 (ppp) cc_final: 0.7370 (ppp) REVERT: B 146 MET cc_start: 0.8906 (tpp) cc_final: 0.8330 (mmm) REVERT: B 245 MET cc_start: 0.7783 (tmm) cc_final: 0.7179 (tmm) REVERT: B 762 MET cc_start: 0.6688 (mmt) cc_final: 0.6293 (mmt) outliers start: 28 outliers final: 20 residues processed: 61 average time/residue: 0.2121 time to fit residues: 24.5548 Evaluate side-chains 53 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 33 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 549 ASN Chi-restraints excluded: chain B residue 589 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 133 optimal weight: 0.5980 chunk 171 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 234 optimal weight: 0.0170 chunk 146 optimal weight: 7.9990 chunk 142 optimal weight: 40.0000 chunk 108 optimal weight: 50.0000 chunk 144 optimal weight: 20.0000 overall best weight: 4.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17457 Z= 0.302 Angle : 0.636 9.815 23940 Z= 0.316 Chirality : 0.044 0.315 3062 Planarity : 0.003 0.032 3139 Dihedral : 7.117 59.763 3249 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 2.45 % Allowed : 14.74 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.17), residues: 2430 helix: -0.80 (0.35), residues: 231 sheet: -2.03 (0.25), residues: 412 loop : -1.31 (0.15), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 31 HIS 0.003 0.001 HIS C 478 PHE 0.012 0.002 PHE C 406 TYR 0.015 0.001 TYR A 79 ARG 0.003 0.000 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 31 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 219 LEU cc_start: 0.8543 (mt) cc_final: 0.8321 (mt) REVERT: C 245 MET cc_start: 0.8197 (tpp) cc_final: 0.7967 (tpp) REVERT: C 624 MET cc_start: 0.2364 (tpp) cc_final: 0.1864 (tpp) REVERT: A 441 MET cc_start: 0.8273 (ppp) cc_final: 0.7525 (ppp) REVERT: B 146 MET cc_start: 0.8927 (tpp) cc_final: 0.8615 (mmm) REVERT: B 245 MET cc_start: 0.7829 (tmm) cc_final: 0.7215 (tmm) REVERT: B 762 MET cc_start: 0.6709 (mmt) cc_final: 0.6320 (mmt) outliers start: 36 outliers final: 29 residues processed: 67 average time/residue: 0.2069 time to fit residues: 26.2636 Evaluate side-chains 60 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 31 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 385 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 489 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 ASN Chi-restraints excluded: chain B residue 589 GLU Chi-restraints excluded: chain B residue 663 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 30.0000 chunk 139 optimal weight: 8.9990 chunk 70 optimal weight: 40.0000 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 148 optimal weight: 40.0000 chunk 159 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17457 Z= 0.323 Angle : 0.646 12.148 23940 Z= 0.320 Chirality : 0.044 0.314 3062 Planarity : 0.003 0.040 3139 Dihedral : 7.157 59.480 3249 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.38 % Allowed : 15.15 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.17), residues: 2430 helix: -0.85 (0.35), residues: 225 sheet: -2.16 (0.24), residues: 417 loop : -1.35 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 491 HIS 0.003 0.001 HIS C 416 PHE 0.013 0.002 PHE C 406 TYR 0.015 0.002 TYR B 79 ARG 0.002 0.000 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 31 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 219 LEU cc_start: 0.8617 (mt) cc_final: 0.8394 (mt) REVERT: C 624 MET cc_start: 0.2327 (tpp) cc_final: 0.1817 (tpp) REVERT: A 441 MET cc_start: 0.8255 (ppp) cc_final: 0.7573 (ppp) REVERT: B 146 MET cc_start: 0.8940 (tpp) cc_final: 0.8629 (mmm) REVERT: B 245 MET cc_start: 0.7807 (tmm) cc_final: 0.7153 (tmm) REVERT: B 762 MET cc_start: 0.6742 (mmt) cc_final: 0.6365 (mmt) outliers start: 35 outliers final: 28 residues processed: 66 average time/residue: 0.2267 time to fit residues: 27.8539 Evaluate side-chains 59 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 31 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 385 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 ASN Chi-restraints excluded: chain B residue 589 GLU Chi-restraints excluded: chain B residue 663 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 197 optimal weight: 0.3980 chunk 206 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17457 Z= 0.245 Angle : 0.602 10.853 23940 Z= 0.299 Chirality : 0.043 0.318 3062 Planarity : 0.003 0.033 3139 Dihedral : 6.932 59.906 3249 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.04 % Allowed : 15.42 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.17), residues: 2430 helix: -0.49 (0.37), residues: 214 sheet: -2.06 (0.24), residues: 424 loop : -1.25 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 491 HIS 0.002 0.001 HIS C 416 PHE 0.011 0.001 PHE B 656 TYR 0.013 0.001 TYR A 79 ARG 0.002 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 32 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 219 LEU cc_start: 0.8624 (mt) cc_final: 0.8392 (mt) REVERT: A 441 MET cc_start: 0.8314 (ppp) cc_final: 0.7715 (ppp) REVERT: B 146 MET cc_start: 0.8923 (tpp) cc_final: 0.8616 (mmm) REVERT: B 245 MET cc_start: 0.7775 (tmm) cc_final: 0.7150 (tmm) REVERT: B 762 MET cc_start: 0.6753 (mmt) cc_final: 0.6398 (mmt) outliers start: 30 outliers final: 26 residues processed: 62 average time/residue: 0.2288 time to fit residues: 26.1880 Evaluate side-chains 58 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 32 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 385 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 ASN Chi-restraints excluded: chain B residue 589 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 9.9990 chunk 140 optimal weight: 50.0000 chunk 109 optimal weight: 50.0000 chunk 160 optimal weight: 0.6980 chunk 242 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 192 optimal weight: 0.0020 chunk 20 optimal weight: 1.9990 chunk 148 optimal weight: 40.0000 chunk 118 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 overall best weight: 3.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17457 Z= 0.239 Angle : 0.604 12.159 23940 Z= 0.297 Chirality : 0.043 0.318 3062 Planarity : 0.003 0.033 3139 Dihedral : 6.833 59.937 3249 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 1.90 % Allowed : 15.56 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2430 helix: -0.39 (0.37), residues: 214 sheet: -2.03 (0.25), residues: 405 loop : -1.25 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 491 HIS 0.002 0.001 HIS C 416 PHE 0.009 0.001 PHE C 406 TYR 0.013 0.001 TYR A 79 ARG 0.004 0.000 ARG B 625 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 31 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 219 LEU cc_start: 0.8698 (mt) cc_final: 0.8476 (mt) REVERT: A 441 MET cc_start: 0.8306 (ppp) cc_final: 0.7725 (ppp) REVERT: B 146 MET cc_start: 0.8916 (tpp) cc_final: 0.8617 (mmm) REVERT: B 245 MET cc_start: 0.7748 (tmm) cc_final: 0.7095 (tmm) REVERT: B 762 MET cc_start: 0.6703 (mmt) cc_final: 0.6347 (mmt) outliers start: 28 outliers final: 28 residues processed: 59 average time/residue: 0.2360 time to fit residues: 25.6536 Evaluate side-chains 59 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 31 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 385 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 ASN Chi-restraints excluded: chain B residue 589 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.0010 chunk 59 optimal weight: 50.0000 chunk 177 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 169 optimal weight: 0.0470 overall best weight: 1.5488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 372 ASN B 444 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.049960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.036552 restraints weight = 147316.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.037523 restraints weight = 78630.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.038178 restraints weight = 52502.684| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17457 Z= 0.152 Angle : 0.564 11.139 23940 Z= 0.278 Chirality : 0.043 0.325 3062 Planarity : 0.003 0.033 3139 Dihedral : 6.490 58.321 3249 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.49 % Allowed : 16.10 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.17), residues: 2430 helix: -0.36 (0.36), residues: 227 sheet: -1.93 (0.25), residues: 397 loop : -1.14 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 491 HIS 0.002 0.000 HIS A 576 PHE 0.012 0.001 PHE D 58 TYR 0.009 0.001 TYR C 65 ARG 0.002 0.000 ARG B 475 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3108.87 seconds wall clock time: 57 minutes 29.36 seconds (3449.36 seconds total)