Starting phenix.real_space_refine on Mon Dec 11 08:40:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1c_11983/12_2023/7b1c_11983.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1c_11983/12_2023/7b1c_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_11983/12_2023/7b1c_11983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1c_11983/12_2023/7b1c_11983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1c_11983/12_2023/7b1c_11983.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b1c_11983/12_2023/7b1c_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 9.62, per 1000 atoms: 0.56 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: 7.55 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: 2.01 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: 5.71 Time building geometry restraints manager: 8.08 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 - 17.61: 10138 17.61 - 35.23: 659 35.23 - 52.84: 134 52.84 - 70.46: 37 70.46 - 88.07: 10 Dihedral angle restraints: 10978 sinusoidal: 3768 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 10975 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: 3.470 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: 0.030 Extract box with map and model: 12.340 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 47.990 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.690 ------------------------------------------------------------------------------- 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 : 12.759 87.104 6148 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 : 2.073 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 8 residues processed: 102 average time/residue: 0.2689 time to fit residues: 45.9385 Evaluate side-chains 46 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 2.513 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1815 time to fit residues: 5.6763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.7804 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17457 Z= 0.263 Angle : 0.664 8.590 23940 Z= 0.336 Chirality : 0.045 0.309 3062 Planarity : 0.004 0.039 3139 Dihedral : 7.884 59.674 3131 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.95 % Allowed : 8.90 % Favored : 90.15 % 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: -1.16 (0.34), residues: 216 sheet: -2.08 (0.23), residues: 456 loop : -1.21 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 491 HIS 0.003 0.001 HIS C 416 PHE 0.012 0.001 PHE C 285 TYR 0.015 0.001 TYR C 440 ARG 0.004 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 51 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 2.120 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 51 average time/residue: 0.2602 time to fit residues: 23.8440 Evaluate side-chains 37 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 1.965 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1486 time to fit residues: 3.7629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 183 optimal weight: 30.0000 chunk 150 optimal weight: 8.9990 chunk 60 optimal weight: 50.0000 chunk 221 optimal weight: 8.9990 chunk 238 optimal weight: 20.0000 chunk 196 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 75 optimal weight: 0.0970 chunk 177 optimal weight: 5.9990 overall best weight: 6.4186 ------------------------------------------------------------------------------- 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 469 GLN ** C 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 17457 Z= 0.475 Angle : 0.805 9.234 23940 Z= 0.399 Chirality : 0.047 0.324 3062 Planarity : 0.004 0.044 3139 Dihedral : 7.961 56.980 3131 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 1.97 % Allowed : 11.75 % Favored : 86.28 % 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: -2.31 (0.17), residues: 2430 helix: -1.37 (0.33), residues: 231 sheet: -2.17 (0.24), residues: 436 loop : -1.45 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 491 HIS 0.006 0.001 HIS B 132 PHE 0.018 0.002 PHE C 55 TYR 0.026 0.002 TYR A 440 ARG 0.004 0.001 ARG B 475 *********************** 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 63 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 34 time to evaluate : 1.895 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 62 average time/residue: 0.2348 time to fit residues: 26.4310 Evaluate side-chains 44 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1604 time to fit residues: 6.2143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 8.9990 chunk 166 optimal weight: 0.2980 chunk 114 optimal weight: 40.0000 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 50.0000 chunk 148 optimal weight: 30.0000 chunk 221 optimal weight: 0.7980 chunk 234 optimal weight: 0.0370 chunk 115 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 63 optimal weight: 50.0000 overall best weight: 2.4262 ------------------------------------------------------------------------------- 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 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 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: 0.7897 moved from start: 0.2327 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= 0.201 Angle : 0.608 8.891 23940 Z= 0.304 Chirality : 0.043 0.311 3062 Planarity : 0.003 0.033 3139 Dihedral : 7.338 59.852 3131 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.95 % Allowed : 13.32 % Favored : 85.73 % 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: -0.87 (0.35), residues: 224 sheet: -2.10 (0.23), residues: 439 loop : -1.25 (0.15), residues: 1767 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 0.010 0.001 PHE D 58 TYR 0.011 0.001 TYR B 79 ARG 0.003 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 49 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 35 time to evaluate : 2.010 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 48 average time/residue: 0.2263 time to fit residues: 21.0264 Evaluate side-chains 39 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 2.156 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1657 time to fit residues: 4.8257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 50.0000 chunk 210 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 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** ** 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: 0.7951 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17457 Z= 0.358 Angle : 0.686 9.825 23940 Z= 0.342 Chirality : 0.045 0.309 3062 Planarity : 0.004 0.033 3139 Dihedral : 7.379 58.183 3131 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 1.77 % Allowed : 14.13 % Favored : 84.10 % 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: -2.21 (0.17), residues: 2430 helix: -1.04 (0.34), residues: 230 sheet: -2.16 (0.25), residues: 403 loop : -1.43 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 31 HIS 0.004 0.001 HIS C 416 PHE 0.013 0.002 PHE A 261 TYR 0.018 0.002 TYR A 79 ARG 0.003 0.000 ARG B 475 *********************** 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 57 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 31 time to evaluate : 2.033 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 7 residues processed: 57 average time/residue: 0.2201 time to fit residues: 24.3066 Evaluate side-chains 38 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 2.093 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1623 time to fit residues: 5.0806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 137 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 195 optimal weight: 0.0870 chunk 108 optimal weight: 50.0000 chunk 19 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 overall best weight: 2.3964 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2803 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= 0.197 Angle : 0.604 10.221 23940 Z= 0.300 Chirality : 0.043 0.317 3062 Planarity : 0.003 0.034 3139 Dihedral : 6.997 59.459 3131 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.88 % Allowed : 15.29 % Favored : 83.83 % 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: -1.93 (0.17), residues: 2430 helix: -0.70 (0.35), residues: 223 sheet: -2.01 (0.24), residues: 431 loop : -1.21 (0.15), residues: 1776 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 0.010 0.001 PHE D 58 TYR 0.011 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 46 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 33 time to evaluate : 2.132 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 46 average time/residue: 0.2353 time to fit residues: 20.8601 Evaluate side-chains 40 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 2.088 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1632 time to fit residues: 5.1014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 131 optimal weight: 0.0370 chunk 234 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 142 optimal weight: 40.0000 chunk 108 optimal weight: 50.0000 chunk 144 optimal weight: 20.0000 overall best weight: 7.6066 ------------------------------------------------------------------------------- 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 560 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 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** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 17457 Z= 0.534 Angle : 0.803 9.941 23940 Z= 0.396 Chirality : 0.047 0.303 3062 Planarity : 0.004 0.035 3139 Dihedral : 7.649 58.644 3131 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 0.88 % Allowed : 16.30 % 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: -2.45 (0.16), residues: 2430 helix: -1.20 (0.34), residues: 226 sheet: -2.40 (0.25), residues: 395 loop : -1.59 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 31 HIS 0.006 0.001 HIS B 132 PHE 0.017 0.002 PHE C 55 TYR 0.022 0.002 TYR B 79 ARG 0.004 0.001 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 44 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 1.976 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 44 average time/residue: 0.2198 time to fit residues: 18.9944 Evaluate side-chains 37 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 2.010 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1600 time to fit residues: 4.7211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 20.0000 chunk 139 optimal weight: 0.0050 chunk 70 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 184 optimal weight: 0.8980 chunk 213 optimal weight: 0.7980 overall best weight: 1.5398 ------------------------------------------------------------------------------- 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 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 385 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17457 Z= 0.171 Angle : 0.598 10.264 23940 Z= 0.297 Chirality : 0.043 0.318 3062 Planarity : 0.003 0.034 3139 Dihedral : 6.964 59.555 3131 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.27 % Allowed : 16.51 % Favored : 83.22 % 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: -2.00 (0.17), residues: 2430 helix: -0.60 (0.36), residues: 224 sheet: -2.12 (0.24), residues: 425 loop : -1.27 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 491 HIS 0.003 0.001 HIS B 323 PHE 0.011 0.001 PHE A 55 TYR 0.010 0.001 TYR A 79 ARG 0.002 0.000 ARG A 733 *********************** 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 36 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 2.060 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 36 average time/residue: 0.2319 time to fit residues: 16.9033 Evaluate side-chains 32 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 2.064 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 218 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 66 optimal weight: 50.0000 chunk 197 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 560 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 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 17457 Z= 0.461 Angle : 0.746 11.284 23940 Z= 0.367 Chirality : 0.046 0.314 3062 Planarity : 0.004 0.042 3139 Dihedral : 7.395 58.124 3131 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 0.48 % Allowed : 16.71 % 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: -2.36 (0.17), residues: 2430 helix: -1.02 (0.34), residues: 227 sheet: -2.37 (0.25), residues: 399 loop : -1.53 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 31 HIS 0.005 0.001 HIS A 662 PHE 0.016 0.002 PHE C 406 TYR 0.017 0.002 TYR A 79 ARG 0.003 0.001 ARG B 475 *********************** 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 38 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 2.111 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 0.2627 time to fit residues: 19.0281 Evaluate side-chains 35 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 2.030 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3121 time to fit residues: 4.5598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 109 optimal weight: 50.0000 chunk 160 optimal weight: 7.9990 chunk 242 optimal weight: 20.0000 chunk 222 optimal weight: 0.0370 chunk 192 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 overall best weight: 4.9464 ------------------------------------------------------------------------------- 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 385 ASN ** 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: 0.7972 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17457 Z= 0.345 Angle : 0.683 11.932 23940 Z= 0.337 Chirality : 0.044 0.318 3062 Planarity : 0.003 0.033 3139 Dihedral : 7.279 58.347 3131 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 16.92 % Favored : 83.08 % 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: -2.31 (0.17), residues: 2430 helix: -0.86 (0.35), residues: 231 sheet: -2.34 (0.24), residues: 424 loop : -1.49 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 491 HIS 0.003 0.001 HIS A 662 PHE 0.013 0.002 PHE C 55 TYR 0.016 0.002 TYR A 79 ARG 0.003 0.000 ARG B 475 ********************** 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 31 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.997 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2374 time to fit residues: 15.3548 Evaluate side-chains 31 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 2.171 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 4.9990 chunk 59 optimal weight: 30.0000 chunk 177 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.049722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.036343 restraints weight = 147793.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.037298 restraints weight = 79664.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.037942 restraints weight = 53393.329| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3480 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 : 0.595 11.617 23940 Z= 0.293 Chirality : 0.043 0.325 3062 Planarity : 0.003 0.033 3139 Dihedral : 6.696 59.011 3131 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 16.85 % Favored : 83.15 % 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: -1.94 (0.17), residues: 2430 helix: -0.42 (0.36), residues: 220 sheet: -2.12 (0.25), residues: 425 loop : -1.24 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 491 HIS 0.002 0.001 HIS B 323 PHE 0.014 0.001 PHE D 58 TYR 0.010 0.001 TYR C 440 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: 2880.48 seconds wall clock time: 53 minutes 41.21 seconds (3221.21 seconds total)