Starting phenix.real_space_refine (version: dev) on Wed Feb 22 10:46:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e98_27959/02_2023/8e98_27959.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e98_27959/02_2023/8e98_27959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e98_27959/02_2023/8e98_27959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e98_27959/02_2023/8e98_27959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e98_27959/02_2023/8e98_27959.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e98_27959/02_2023/8e98_27959.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.002 sd= 0.097 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 Process input model Symmetric amino acids flipped Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "A PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 739": "OE1" <-> "OE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ASP 460": "OD1" <-> "OD2" Residue "B ASP 698": "OD1" <-> "OD2" Residue "B TYR 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 774": "OD1" <-> "OD2" Residue "B ASP 783": "OD1" <-> "OD2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 511": "OD1" <-> "OD2" Residue "C TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 787": "OD1" <-> "OD2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 698": "OD1" <-> "OD2" Residue "D ASP 740": "OD1" <-> "OD2" Residue "D ASP 783": "OD1" <-> "OD2" Residue "D GLU 785": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 17208 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 4109 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 273} Link IDs: {'PTRANS': 27, 'TRANS': 620} Chain breaks: 2 Unresolved non-hydrogen bonds: 1080 Unresolved non-hydrogen angles: 1352 Unresolved non-hydrogen dihedrals: 887 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 22, 'TYR:plan': 9, 'ASN:plan1': 26, 'TRP:plan': 2, 'HIS:plan': 11, 'PHE:plan': 8, 'GLU:plan': 38, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 674 Chain: "B" Number of atoms: 3965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 3965 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PTRANS': 38, 'TRANS': 603} Chain breaks: 2 Unresolved non-hydrogen bonds: 1059 Unresolved non-hydrogen angles: 1357 Unresolved non-hydrogen dihedrals: 882 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 7, 'ASP:plan': 19, 'PHE:plan': 13, 'GLU:plan': 24, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 667 Chain: "C" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 4464 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 188} Link IDs: {'PTRANS': 29, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 753 Unresolved non-hydrogen angles: 918 Unresolved non-hydrogen dihedrals: 624 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 18, 'TYR:plan': 3, 'ASN:plan1': 19, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 3, 'GLU:plan': 39, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 512 Chain: "D" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4427 Classifications: {'peptide': 638} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 39, 'TRANS': 598} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 532 Unresolved non-hydrogen angles: 652 Unresolved non-hydrogen dihedrals: 440 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 4, 'GLU:plan': 20, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 380 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: 1 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" 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 chiralities: 1 Time building chain proxies: 10.77, per 1000 atoms: 0.63 Number of scatterers: 17208 At special positions: 0 Unit cell: (130.968, 144.664, 135.248, 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 67 16.00 O 3245 8.00 N 2961 7.00 C 10935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 317 " distance=2.03 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 453 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.05 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 317 " distance=2.04 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.04 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 798 " 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=1, 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 G 2 " - " BMA G 3 " NAG-ASN " NAG A 902 " - " ASN A 771 " " NAG A 903 " - " ASN A 471 " " NAG B 901 " - " ASN B 337 " " NAG C 902 " - " ASN C 771 " " NAG C 903 " - " ASN C 350 " " NAG C 904 " - " ASN C 276 " " NAG D 901 " - " ASN D 337 " " NAG F 1 " - " ASN B 685 " " NAG G 1 " - " ASN C 61 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.98 Conformation dependent library (CDL) restraints added in 3.1 seconds 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4786 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 29 sheets defined 37.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 37 through 53 removed outlier: 3.718A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.926A pdb=" N SER A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.694A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 159 removed outlier: 4.265A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.904A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.604A pdb=" N ALA A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 296 removed outlier: 4.051A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.083A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.654A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.082A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 removed outlier: 3.815A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.582A pdb=" N GLU A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 783 removed outlier: 3.724A pdb=" N GLY A 783 " --> pdb=" O SER A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 73 through 89 Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.530A pdb=" N GLN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.577A pdb=" N ARG B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.617A pdb=" N GLN B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 removed outlier: 4.159A pdb=" N GLU B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 306 removed outlier: 3.745A pdb=" N GLN B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 removed outlier: 3.734A pdb=" N TYR B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.573A pdb=" N ASN B 691 " --> pdb=" O SER B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 703 removed outlier: 4.153A pdb=" N HIS B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 removed outlier: 3.637A pdb=" N THR B 716 " --> pdb=" O GLU B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 739 Processing helix chain 'B' and resid 748 through 752 Processing helix chain 'B' and resid 768 through 783 removed outlier: 4.275A pdb=" N ALA B 772 " --> pdb=" O HIS B 768 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 794 Processing helix chain 'C' and resid 36 through 53 removed outlier: 3.903A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 85 Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.810A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 removed outlier: 3.618A pdb=" N HIS C 146 " --> pdb=" O PRO C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 146' Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.537A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 187 removed outlier: 4.039A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 177 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.820A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.851A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 4.118A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 297 removed outlier: 3.530A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 457 through 470 Processing helix chain 'C' and resid 500 through 508 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.825A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 695 removed outlier: 3.989A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 707 removed outlier: 3.565A pdb=" N THR C 701 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 783 Processing helix chain 'C' and resid 783 through 793 removed outlier: 3.533A pdb=" N ASP C 787 " --> pdb=" O GLY C 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.671A pdb=" N LEU D 108 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 161 removed outlier: 3.989A pdb=" N GLU D 159 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 187 removed outlier: 3.589A pdb=" N ARG D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 218 removed outlier: 3.771A pdb=" N THR D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 284 through 308 removed outlier: 3.561A pdb=" N GLN D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 456 through 470 Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 513 through 520 removed outlier: 3.837A pdb=" N ILE D 519 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 696 through 703 Processing helix chain 'D' and resid 712 through 721 removed outlier: 3.541A pdb=" N THR D 716 " --> pdb=" O GLU D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 737 removed outlier: 3.842A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 784 removed outlier: 3.985A pdb=" N ALA D 772 " --> pdb=" O HIS D 768 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 775 " --> pdb=" O ARG D 771 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP D 783 " --> pdb=" O GLN D 779 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY D 784 " --> pdb=" O PHE D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 794 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 7.357A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.411A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.334A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.524A pdb=" N GLY A 268 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 478 removed outlier: 3.520A pdb=" N ILE A 400 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 528 through 529 removed outlier: 4.360A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 409 through 412 Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.279A pdb=" N VAL B 32 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL B 67 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL B 34 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200 removed outlier: 7.197A pdb=" N PHE B 165 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N VAL B 199 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL B 167 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA B 164 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL B 225 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA B 166 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N TYR B 227 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE B 168 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 276 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU B 273 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 363 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 360 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 406 removed outlier: 3.654A pdb=" N ALA B 406 " --> pdb=" O MET B 505 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 414 through 417 removed outlier: 3.607A pdb=" N GLU B 417 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 453 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 452 " --> pdb=" O CYS B 433 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 725 through 728 removed outlier: 7.072A pdb=" N THR B 529 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N THR B 756 " --> pdb=" O THR B 529 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 66 removed outlier: 7.916A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 194 through 197 removed outlier: 6.842A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 219 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 248 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 268 through 270 removed outlier: 6.927A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.039A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC1, first strand: chain 'C' and resid 486 through 489 Processing sheet with id=AC2, first strand: chain 'C' and resid 527 through 528 removed outlier: 3.651A pdb=" N MET C 762 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AC4, first strand: chain 'C' and resid 730 through 732 removed outlier: 3.817A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 64 through 68 removed outlier: 6.193A pdb=" N VAL D 32 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL D 67 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL D 34 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA D 33 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE D 93 " --> pdb=" O LEU D 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 197 through 201 Processing sheet with id=AC7, first strand: chain 'D' and resid 274 through 277 removed outlier: 3.576A pdb=" N GLY D 373 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA D 362 " --> pdb=" O MET D 371 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N MET D 371 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 379 " --> pdb=" O GLU D 376 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 337 through 340 removed outlier: 3.672A pdb=" N TRP D 340 " --> pdb=" O ARG D 343 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER D 346 " --> pdb=" O VAL D 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 415 through 417 removed outlier: 3.627A pdb=" N GLU D 417 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 431 " --> pdb=" O CYS D 454 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU D 475 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG D 434 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 407 " --> pdb=" O TYR D 476 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET D 505 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 762 " --> pdb=" O ALA D 506 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 486 through 487 Processing sheet with id=AD2, first strand: chain 'D' and resid 532 through 534 722 hydrogen bonds defined for protein. 2073 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: 5.82 Time building geometry restraints manager: 8.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.24: 2639 1.24 - 1.56: 14828 1.56 - 1.88: 102 1.88 - 2.21: 0 2.21 - 2.53: 1 Bond restraints: 17570 Sorted by residual: bond pdb=" CB PRO B 356 " pdb=" CG PRO B 356 " ideal model delta sigma weight residual 1.492 2.527 -1.035 5.00e-02 4.00e+02 4.28e+02 bond pdb=" CG PRO B 356 " pdb=" CD PRO B 356 " ideal model delta sigma weight residual 1.503 0.919 0.584 3.40e-02 8.65e+02 2.95e+02 bond pdb=" CG PRO B 448 " pdb=" CD PRO B 448 " ideal model delta sigma weight residual 1.503 1.097 0.406 3.40e-02 8.65e+02 1.43e+02 bond pdb=" N PRO B 356 " pdb=" CD PRO B 356 " ideal model delta sigma weight residual 1.473 1.560 -0.087 1.40e-02 5.10e+03 3.91e+01 bond pdb=" CA PRO B 356 " pdb=" CB PRO B 356 " ideal model delta sigma weight residual 1.533 1.448 0.086 1.42e-02 4.96e+03 3.64e+01 ... (remaining 17565 not shown) Histogram of bond angle deviations from ideal: 11.07 - 38.15: 1 38.15 - 65.23: 0 65.23 - 92.30: 5 92.30 - 119.38: 14798 119.38 - 146.46: 9406 Bond angle restraints: 24210 Sorted by residual: angle pdb=" CB PRO B 356 " pdb=" CG PRO B 356 " pdb=" CD PRO B 356 " ideal model delta sigma weight residual 106.10 11.07 95.03 3.20e+00 9.77e-02 8.82e+02 angle pdb=" N PRO B 448 " pdb=" CD PRO B 448 " pdb=" CG PRO B 448 " ideal model delta sigma weight residual 103.20 70.54 32.66 1.50e+00 4.44e-01 4.74e+02 angle pdb=" CA PRO B 448 " pdb=" CB PRO B 448 " pdb=" CG PRO B 448 " ideal model delta sigma weight residual 104.50 67.02 37.48 1.90e+00 2.77e-01 3.89e+02 angle pdb=" N PRO B 356 " pdb=" CA PRO B 356 " pdb=" CB PRO B 356 " ideal model delta sigma weight residual 103.25 87.38 15.87 1.05e+00 9.07e-01 2.29e+02 angle pdb=" CB PRO B 448 " pdb=" CG PRO B 448 " pdb=" CD PRO B 448 " ideal model delta sigma weight residual 106.10 146.46 -40.36 3.20e+00 9.77e-02 1.59e+02 ... (remaining 24205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.99: 9747 25.99 - 51.98: 433 51.98 - 77.96: 36 77.96 - 103.95: 18 103.95 - 129.94: 4 Dihedral angle restraints: 10238 sinusoidal: 2817 harmonic: 7421 Sorted by residual: dihedral pdb=" CA GLN B 355 " pdb=" C GLN B 355 " pdb=" N PRO B 356 " pdb=" CA PRO B 356 " ideal model delta harmonic sigma weight residual 180.00 141.00 39.00 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 308 " pdb=" CB CYS C 308 " ideal model delta sinusoidal sigma weight residual -86.00 -23.16 -62.84 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 308 " pdb=" CB CYS A 308 " ideal model delta sinusoidal sigma weight residual -86.00 -146.53 60.53 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 10235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2776 0.086 - 0.172: 252 0.172 - 0.258: 6 0.258 - 0.344: 2 0.344 - 0.430: 1 Chirality restraints: 3037 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 685 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA PRO B 356 " pdb=" N PRO B 356 " pdb=" C PRO B 356 " pdb=" CB PRO B 356 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 3034 not shown) Planarity restraints: 3134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 131 " -0.110 5.00e-02 4.00e+02 1.56e-01 3.89e+01 pdb=" N PRO B 132 " 0.269 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 685 " -0.010 2.00e-02 2.50e+03 5.15e-02 3.31e+01 pdb=" CG ASN B 685 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN B 685 " -0.059 2.00e-02 2.50e+03 pdb=" ND2 ASN B 685 " 0.059 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 438 " 0.081 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO C 439 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO C 439 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 439 " 0.061 5.00e-02 4.00e+02 ... (remaining 3131 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 578 2.70 - 3.25: 17096 3.25 - 3.80: 25285 3.80 - 4.35: 28136 4.35 - 4.90: 49599 Nonbonded interactions: 120694 Sorted by model distance: nonbonded pdb=" O LEU C 325 " pdb=" OG SER C 328 " model vdw 2.155 2.440 nonbonded pdb=" O VAL A 684 " pdb=" OG SER A 687 " model vdw 2.226 2.440 nonbonded pdb=" ND2 ASN C 70 " pdb=" O ARG D 318 " model vdw 2.230 2.520 nonbonded pdb=" O ASN B 73 " pdb=" OG SER B 76 " model vdw 2.250 2.440 nonbonded pdb=" O SER A 55 " pdb=" OG SER A 55 " model vdw 2.255 2.440 ... (remaining 120689 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 25 through 26 and (name N or name CA or name C or name O \ or name CB )) or resid 27 through 34 or (resid 35 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 82 or (resid 83 and (n \ ame N or name CA or name C or name O or name CB )) or resid 84 through 158 or (r \ esid 159 and (name N or name CA or name C or name O or name CB )) or resid 160 t \ hrough 331 or (resid 332 and (name N or name CA or name C or name O or name CB ) \ ) or resid 333 through 358 or (resid 359 through 361 and (name N or name CA or n \ ame C or name O or name CB )) or resid 362 through 398 or (resid 399 and (name N \ or name CA or name C or name O or name CB )) or resid 400 through 411 or (resid \ 412 and (name N or name CA or name C or name O or name CB )) or resid 413 throu \ gh 414 or (resid 415 and (name N or name CA or name C or name O or name CB )) or \ resid 416 through 418 or (resid 419 and (name N or name CA or name C or name O \ or name CB )) or resid 420 through 421 or (resid 422 through 423 and (name N or \ name CA or name C or name O or name CB )) or resid 424 through 486 or (resid 487 \ through 497 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 98 through 508 or (resid 509 through 510 and (name N or name CA or name C or nam \ e O or name CB )) or resid 511 through 524 or (resid 525 and (name N or name CA \ or name C or name O or name CB )) or resid 526 through 527 or (resid 528 and (na \ me N or name CA or name C or name O or name CB )) or resid 529 through 535 or (r \ esid 536 and (name N or name CA or name C or name O or name CB )) or resid 537 t \ hrough 666 or (resid 667 through 669 and (name N or name CA or name C or name O \ or name CB )) or resid 670 through 678 or (resid 679 and (name N or name CA or n \ ame C or name O or name CB )) or resid 680 or (resid 681 through 682 and (name N \ or name CA or name C or name O or name CB )) or resid 683 through 684 or (resid \ 685 and (name N or name CA or name C or name O or name CB )) or resid 686 throu \ gh 693 or (resid 694 through 699 and (name N or name CA or name C or name O or n \ ame CB )) or resid 700 through 702 or (resid 703 through 710 and (name N or name \ CA or name C or name O or name CB )) or resid 711 or (resid 712 and (name N or \ name CA or name C or name O or name CB )) or resid 713 through 717 or (resid 718 \ through 728 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 29 through 735 or (resid 736 through 740 and (name N or name CA or name C or nam \ e O or name CB )) or resid 741 through 751 or (resid 752 and (name N or name CA \ or name C or name O or name CB )) or resid 753 through 754 or (resid 755 and (na \ me N or name CA or name C or name O or name CB )) or resid 756 through 762 or (r \ esid 763 and (name N or name CA or name C or name O or name CB )) or resid 764 t \ hrough 777 or (resid 778 and (name N or name CA or name C or name O or name CB ) \ ) or resid 779 through 780 or (resid 781 and (name N or name CA or name C or nam \ e O or name CB )) or resid 782 through 788 or (resid 789 through 790 and (name N \ or name CA or name C or name O or name CB )) or resid 791 through 797 or resid \ 901 through 903)) selection = (chain 'C' and (resid 25 through 27 or (resid 28 through 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 32 or (resid 33 and (na \ me N or name CA or name C or name O or name CB )) or resid 34 through 37 or (res \ id 38 through 45 and (name N or name CA or name C or name O or name CB )) or res \ id 46 through 52 or (resid 53 and (name N or name CA or name C or name O or name \ CB )) or resid 54 through 57 or (resid 58 through 63 and (name N or name CA or \ name C or name O or name CB )) or resid 64 through 67 or (resid 68 and (name N o \ r name CA or name C or name O or name CB )) or resid 69 or (resid 70 through 75 \ and (name N or name CA or name C or name O or name CB )) or resid 76 through 77 \ or (resid 78 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 9 through 80 or (resid 81 and (name N or name CA or name C or name O or name CB \ )) or resid 82 through 87 or (resid 88 through 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 through 100 or (resid 101 through 102 and \ (name N or name CA or name C or name O or name CB )) or resid 103 through 108 o \ r (resid 109 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 10 through 113 or (resid 114 through 116 and (name N or name CA or name C or nam \ e O or name CB )) or resid 117 through 120 or (resid 121 and (name N or name CA \ or name C or name O or name CB )) or resid 122 or (resid 123 through 124 and (na \ me N or name CA or name C or name O or name CB )) or resid 125 or (resid 126 thr \ ough 127 and (name N or name CA or name C or name O or name CB )) or resid 128 t \ hrough 130 or (resid 131 and (name N or name CA or name C or name O or name CB ) \ ) or resid 132 through 134 or (resid 135 and (name N or name CA or name C or nam \ e O or name CB )) or resid 136 or (resid 137 through 138 and (name N or name CA \ or name C or name O or name CB )) or resid 139 through 146 or (resid 147 and (na \ me N or name CA or name C or name O or name CB )) or resid 148 through 151 or (r \ esid 152 through 157 and (name N or name CA or name C or name O or name CB )) or \ resid 158 through 161 or (resid 162 through 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 or (resid 165 and (name N or name CA or n \ ame C or name O or name CB )) or resid 166 or (resid 167 through 172 and (name N \ or name CA or name C or name O or name CB )) or (resid 173 through 188 and (nam \ e N or name CA or name C or name O or name CB )) or resid 189 through 191 or (re \ sid 192 through 193 and (name N or name CA or name C or name O or name CB )) or \ resid 194 or (resid 195 through 198 and (name N or name CA or name C or name O o \ r name CB )) or resid 199 through 204 or (resid 205 through 206 and (name N or n \ ame CA or name C or name O or name CB )) or resid 207 or (resid 208 through 216 \ and (name N or name CA or name C or name O or name CB )) or resid 217 through 21 \ 8 or (resid 219 through 221 and (name N or name CA or name C or name O or name C \ B )) or resid 222 through 224 or (resid 225 through 229 and (name N or name CA o \ r name C or name O or name CB )) or resid 230 or (resid 231 through 238 and (nam \ e N or name CA or name C or name O or name CB )) or resid 239 through 245 or (re \ sid 246 through 248 and (name N or name CA or name C or name O or name CB )) or \ resid 249 through 253 or (resid 254 and (name N or name CA or name C or name O o \ r name CB )) or resid 255 through 256 or (resid 257 through 262 and (name N or n \ ame CA or name C or name O or name CB )) or resid 263 through 265 or (resid 266 \ through 267 and (name N or name CA or name C or name O or name CB )) or resid 26 \ 8 or (resid 269 through 273 and (name N or name CA or name C or name O or name C \ B )) or (resid 274 through 277 and (name N or name CA or name C or name O or nam \ e CB )) or resid 278 through 279 or (resid 280 through 281 and (name N or name C \ A or name C or name O or name CB )) or resid 282 or (resid 283 through 285 and ( \ name N or name CA or name C or name O or name CB )) or resid 286 or (resid 287 t \ hrough 291 and (name N or name CA or name C or name O or name CB )) or resid 292 \ through 294 or (resid 295 through 303 and (name N or name CA or name C or name \ O or name CB )) or resid 304 through 313 or (resid 314 and (name N or name CA or \ name C or name O or name CB )) or resid 315 through 319 or (resid 320 through 3 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 327 through \ 329 or (resid 330 through 332 and (name N or name CA or name C or name O or nam \ e CB )) or resid 333 through 336 or (resid 337 and (name N or name CA or name C \ or name O or name CB )) or resid 338 or (resid 339 through 343 and (name N or na \ me CA or name C or name O or name CB )) or (resid 344 through 349 and (name N or \ name CA or name C or name O or name CB )) or resid 350 or (resid 351 and (name \ N or name CA or name C or name O or name CB )) or resid 352 or (resid 353 throug \ h 361 and (name N or name CA or name C or name O or name CB )) or resid 362 or ( \ resid 363 and (name N or name CA or name C or name O or name CB )) or resid 364 \ through 366 or (resid 367 and (name N or name CA or name C or name O or name CB \ )) or resid 368 through 378 or (resid 379 and (name N or name CA or name C or na \ me O or name CB )) or resid 380 through 385 or (resid 386 through 388 and (name \ N or name CA or name C or name O or name CB )) or resid 389 through 425 or (resi \ d 426 through 427 and (name N or name CA or name C or name O or name CB )) or re \ sid 428 through 440 or resid 448 through 519 or (resid 520 and (name N or name C \ A or name C or name O or name CB )) or resid 521 through 540 or (resid 541 and ( \ name N or name CA or name C or name O or name CB )) or resid 542 through 663 or \ (resid 664 through 665 and (name N or name CA or name C or name O or name CB )) \ or (resid 666 through 669 and (name N or name CA or name C or name O or name CB \ )) or resid 670 through 671 or (resid 672 through 674 and (name N or name CA or \ name C or name O or name CB )) or resid 675 through 694 or (resid 695 through 69 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 700 through \ 786 or (resid 787 and (name N or name CA or name C or name O or name CB )) or re \ sid 788 through 797 or resid 901 through 903)) } ncs_group { reference = (chain 'B' and (resid 31 through 53 or (resid 54 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 202 or (resid 203 and ( \ name N or name CA or name C or name O or name CB )) or resid 204 through 284 or \ (resid 285 through 291 and (name N or name CA or name C or name O or name CB )) \ or resid 292 through 305 or (resid 306 through 307 and (name N or name CA or nam \ e C or name O or name CB )) or resid 308 through 408 or (resid 409 through 411 a \ nd (name N or name CA or name C or name O or name CB )) or resid 412 through 416 \ or (resid 417 and (name N or name CA or name C or name O or name CB )) or resid \ 418 through 435 or (resid 436 and (name N or name CA or name C or name O or nam \ e CB )) or resid 437 or (resid 447 through 449 and (name N or name CA or name C \ or name O or name CB )) or resid 450 through 481 or (resid 482 and (name N or na \ me CA or name C or name O or name CB )) or resid 483 through 500 or (resid 501 a \ nd (name N or name CA or name C or name O or name CB )) or resid 502 through 537 \ or resid 659 through 667 or (resid 668 through 670 and (name N or name CA or na \ me C or name O or name CB )) or resid 671 through 698 or (resid 699 through 700 \ and (name N or name CA or name C or name O or name CB )) or resid 701 or (resid \ 702 through 703 and (name N or name CA or name C or name O or name CB )) or resi \ d 704 through 705 or (resid 706 through 709 and (name N or name CA or name C or \ name O or name CB )) or resid 710 through 723 or (resid 724 through 725 and (nam \ e N or name CA or name C or name O or name CB )) or resid 726 through 773 or (re \ sid 774 and (name N or name CA or name C or name O or name CB )) or resid 775 th \ rough 786 or (resid 787 through 788 and (name N or name CA or name C or name O o \ r name CB )) or resid 789 or (resid 790 and (name N or name CA or name C or name \ O or name CB )) or resid 791 through 798 or resid 901)) selection = (chain 'D' and ((resid 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 or (resid 38 through 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 through 50 or (resid 51 and \ (name N or name CA or name C or name O or name CB )) or resid 52 through 64 or ( \ resid 65 and (name N or name CA or name C or name O or name CB )) or resid 66 or \ (resid 67 and (name N or name CA or name C or name O or name CB )) or resid 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 77 or (resid 78 and (name N or name CA or name C or name O \ or name CB )) or resid 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 89 or (resid 90 through 91 and (n \ ame N or name CA or name C or name O or name CB )) or resid 92 or (resid 93 thro \ ugh 111 and (name N or name CA or name C or name O or name CB )) or resid 112 th \ rough 113 or (resid 114 through 117 and (name N or name CA or name C or name O o \ r name CB )) or resid 118 or (resid 119 through 120 and (name N or name CA or na \ me C or name O or name CB )) or resid 121 or (resid 122 through 123 and (name N \ or name CA or name C or name O or name CB )) or resid 124 through 125 or (resid \ 126 through 131 and (name N or name CA or name C or name O or name CB )) or resi \ d 132 through 136 or (resid 137 through 142 and (name N or name CA or name C or \ name O or name CB )) or resid 143 or (resid 144 and (name N or name CA or name C \ or name O or name CB )) or resid 145 or (resid 146 through 162 and (name N or n \ ame CA or name C or name O or name CB )) or resid 163 through 164 or (resid 165 \ through 166 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 7 or (resid 168 and (name N or name CA or name C or name O or name CB )) or resi \ d 169 through 170 or (resid 171 through 172 and (name N or name CA or name C or \ name O or name CB )) or resid 173 through 174 or (resid 175 through 178 and (nam \ e N or name CA or name C or name O or name CB )) or resid 179 through 181 or (re \ sid 182 through 197 and (name N or name CA or name C or name O or name CB )) or \ resid 198 through 212 or (resid 213 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 n \ ame CA or name C or name O or name CB )) or resid 229 or (resid 230 through 234 \ and (name N or name CA or name C or name O or name CB )) or resid 235 through 23 \ 8 or (resid 239 through 243 and (name N or name CA or name C or name O or name C \ B )) or resid 244 or (resid 245 through 246 and (name N or name CA or name C or \ name O or name CB )) or resid 247 through 249 or (resid 250 and (name N or name \ CA or name C or name O or name CB )) or resid 251 through 252 or (resid 253 and \ (name N or name CA or name C or name O or name CB )) or resid 254 through 258 or \ (resid 259 and (name N or name CA or name C or name O or name CB )) or resid 26 \ 0 through 262 or (resid 263 through 264 and (name N or name CA or name C or name \ O or name CB )) or resid 265 through 267 or (resid 268 and (name N or name CA o \ r name C or name O or name CB )) or resid 269 through 270 or (resid 271 and (nam \ e N or name CA or name C or name O or name CB )) or resid 272 or (resid 273 thro \ ugh 274 and (name N or name CA or name C or name O or name CB )) or resid 275 or \ (resid 276 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 7 through 278 or (resid 279 and (name N or name CA or name C or name O or name C \ B )) or resid 280 through 282 or (resid 283 and (name N or name CA or name C or \ name O or name CB )) or resid 284 through 286 or (resid 287 through 291 and (nam \ e N or name CA or name C or name O or name CB )) or resid 292 or (resid 293 thro \ ugh 298 and (name N or name CA or name C or name O or name CB )) or resid 299 th \ rough 303 or (resid 304 through 307 and (name N or name CA or name C or name O o \ r name CB )) or resid 308 through 331 or (resid 332 through 336 and (name N or n \ ame CA or name C or name O or name CB )) or resid 337 or (resid 338 through 341 \ and (name N or name CA or name C or name O or name CB )) or (resid 342 through 3 \ 45 and (name N or name CA or name C or name O or name CB )) or resid 346 or (res \ id 347 and (name N or name CA or name C or name O or name CB )) or resid 348 thr \ ough 351 or (resid 352 through 355 and (name N or name CA or name C or name O or \ name CB )) or resid 356 or (resid 357 through 358 and (name N or name CA or nam \ e C or name O or name CB )) or resid 359 or (resid 360 through 371 and (name N o \ r name CA or name C or name O or name CB )) or resid 372 through 373 or (resid 3 \ 74 through 377 and (name N or name CA or name C or name O or name CB )) or resid \ 378 through 379 or (resid 380 and (name N or name CA or name C or name O or nam \ e CB )) or resid 381 or (resid 382 through 383 and (name N or name CA or name C \ or name O or name CB )) or resid 384 through 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 or (resid 389 through 390 a \ nd (name N or name CA or name C or name O or name CB )) or resid 391 or (resid 3 \ 99 and (name N or name CA or name C or name O or name CB )) or resid 400 or (res \ id 401 and (name N or name CA or name C or name O or name CB )) or resid 402 thr \ ough 422 or (resid 423 and (name N or name CA or name C or name O or name CB )) \ or resid 424 through 428 or (resid 429 and (name N or name CA or name C or name \ O or name CB )) or resid 430 through 433 or (resid 434 and (name N or name CA or \ name C or name O or name CB )) or resid 435 through 448 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 454 or (res \ id 455 and (name N or name CA or name C or name O or name CB )) or resid 456 thr \ ough 514 or (resid 515 and (name N or name CA or name C or name O or name CB )) \ or resid 516 through 527 or (resid 528 and (name N or name CA or name C or name \ O or name CB )) or resid 529 through 679 or (resid 680 and (name N or name CA or \ name C or name O or name CB )) or resid 681 through 689 or (resid 690 and (name \ N or name CA or name C or name O or name CB )) or resid 691 through 692 or (res \ id 693 and (name N or name CA or name C or name O or name CB )) or resid 694 thr \ ough 796 or (resid 797 and (name N or name CA or name C or name O or name CB )) \ or resid 798 or resid 901)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 10935 2.51 5 N 2961 2.21 5 O 3245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.870 Check model and map are aligned: 0.290 Process input model: 48.900 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.011 1.035 17570 Z= 0.774 Angle : 1.073 95.030 24210 Z= 0.525 Chirality : 0.046 0.430 3037 Planarity : 0.006 0.156 3125 Dihedral : 15.317 129.940 5413 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.89 % Favored : 92.07 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -1.29 (0.17), residues: 2561 helix: 1.11 (0.18), residues: 841 sheet: -1.19 (0.27), residues: 400 loop : -2.15 (0.17), residues: 1320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.2934 time to fit residues: 80.5542 Evaluate side-chains 156 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.128 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.2980 chunk 149 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 770 GLN D 175 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.092 17570 Z= 0.523 Angle : 0.818 11.956 24210 Z= 0.435 Chirality : 0.053 0.707 3037 Planarity : 0.006 0.084 3125 Dihedral : 9.676 109.484 2801 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.45 % Favored : 90.47 % Rotamer Outliers : 9.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.49 (0.17), residues: 2561 helix: 0.82 (0.18), residues: 865 sheet: -1.33 (0.27), residues: 400 loop : -2.23 (0.17), residues: 1296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 158 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 85 residues processed: 271 average time/residue: 0.2471 time to fit residues: 108.0622 Evaluate side-chains 228 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 143 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 1 residues processed: 85 average time/residue: 0.1642 time to fit residues: 28.6234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 40.0000 chunk 232 optimal weight: 20.0000 chunk 251 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 270 GLN ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 17570 Z= 0.277 Angle : 0.655 10.162 24210 Z= 0.342 Chirality : 0.049 0.762 3037 Planarity : 0.005 0.073 3125 Dihedral : 9.458 109.362 2801 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer Outliers : 2.93 % 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: -1.26 (0.17), residues: 2561 helix: 1.03 (0.18), residues: 874 sheet: -1.26 (0.27), residues: 420 loop : -2.11 (0.17), residues: 1267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 160 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 17 residues processed: 192 average time/residue: 0.2687 time to fit residues: 82.6708 Evaluate side-chains 165 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 2.261 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1693 time to fit residues: 7.9797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 122 optimal weight: 0.0970 chunk 221 optimal weight: 0.1980 chunk 66 optimal weight: 50.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 17570 Z= 0.280 Angle : 0.641 9.018 24210 Z= 0.334 Chirality : 0.048 0.650 3037 Planarity : 0.005 0.073 3125 Dihedral : 9.375 109.425 2801 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.79 % Favored : 91.14 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2561 helix: 1.12 (0.18), residues: 881 sheet: -1.26 (0.26), residues: 423 loop : -2.10 (0.17), residues: 1257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 156 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 27 residues processed: 194 average time/residue: 0.2633 time to fit residues: 81.7791 Evaluate side-chains 175 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 2.099 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1624 time to fit residues: 11.0243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 126 optimal weight: 0.0170 chunk 222 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 overall best weight: 0.4620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 17570 Z= 0.178 Angle : 0.595 10.037 24210 Z= 0.304 Chirality : 0.047 0.737 3037 Planarity : 0.004 0.072 3125 Dihedral : 9.207 109.238 2801 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.24 % Rotamer Outliers : 2.20 % 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: -1.09 (0.17), residues: 2561 helix: 1.21 (0.18), residues: 885 sheet: -1.26 (0.26), residues: 431 loop : -2.01 (0.18), residues: 1245 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 10 residues processed: 191 average time/residue: 0.2752 time to fit residues: 83.9240 Evaluate side-chains 154 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1696 time to fit residues: 5.7042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 4.9990 chunk 222 optimal weight: 30.0000 chunk 48 optimal weight: 0.0010 chunk 145 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 247 optimal weight: 0.0570 chunk 205 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 81 optimal weight: 0.3980 chunk 130 optimal weight: 6.9990 overall best weight: 0.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 17570 Z= 0.174 Angle : 0.596 13.224 24210 Z= 0.302 Chirality : 0.046 0.565 3037 Planarity : 0.004 0.072 3125 Dihedral : 9.124 109.139 2801 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.18 % Favored : 92.74 % Rotamer Outliers : 1.03 % 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: -0.94 (0.17), residues: 2561 helix: 1.38 (0.18), residues: 875 sheet: -1.09 (0.26), residues: 419 loop : -1.97 (0.18), residues: 1267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 167 average time/residue: 0.2623 time to fit residues: 70.4940 Evaluate side-chains 151 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1477 time to fit residues: 4.3450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.9980 chunk 27 optimal weight: 0.0020 chunk 141 optimal weight: 0.1980 chunk 180 optimal weight: 10.0000 chunk 140 optimal weight: 0.0670 chunk 208 optimal weight: 3.9990 chunk 138 optimal weight: 0.4980 chunk 246 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.3526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.061 17570 Z= 0.167 Angle : 0.591 11.428 24210 Z= 0.299 Chirality : 0.046 0.639 3037 Planarity : 0.004 0.072 3125 Dihedral : 9.059 109.047 2801 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.83 % Favored : 93.09 % Rotamer Outliers : 1.32 % 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: -0.85 (0.17), residues: 2561 helix: 1.42 (0.18), residues: 876 sheet: -1.00 (0.26), residues: 420 loop : -1.92 (0.18), residues: 1265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 167 average time/residue: 0.2775 time to fit residues: 73.4556 Evaluate side-chains 151 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 2.030 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1784 time to fit residues: 4.8854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 147 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 156 optimal weight: 0.2980 chunk 168 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 193 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 17570 Z= 0.184 Angle : 0.591 11.674 24210 Z= 0.299 Chirality : 0.045 0.413 3037 Planarity : 0.004 0.072 3125 Dihedral : 9.037 109.073 2801 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.83 % Favored : 93.09 % Rotamer Outliers : 0.88 % 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: -0.76 (0.17), residues: 2561 helix: 1.56 (0.18), residues: 875 sheet: -0.96 (0.26), residues: 422 loop : -1.91 (0.18), residues: 1264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 164 average time/residue: 0.2962 time to fit residues: 76.5955 Evaluate side-chains 154 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1585 time to fit residues: 4.1096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 70 optimal weight: 50.0000 chunk 207 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 17570 Z= 0.250 Angle : 0.631 12.072 24210 Z= 0.321 Chirality : 0.046 0.444 3037 Planarity : 0.004 0.072 3125 Dihedral : 9.116 109.365 2801 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.97 % Favored : 91.96 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2561 helix: 1.53 (0.18), residues: 882 sheet: -0.87 (0.27), residues: 409 loop : -1.92 (0.18), residues: 1270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 149 average time/residue: 0.2927 time to fit residues: 69.1479 Evaluate side-chains 149 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1728 time to fit residues: 4.8347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 255 optimal weight: 0.7980 chunk 234 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 21 optimal weight: 50.0000 chunk 156 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 17570 Z= 0.224 Angle : 0.615 12.384 24210 Z= 0.311 Chirality : 0.046 0.460 3037 Planarity : 0.004 0.072 3125 Dihedral : 9.107 109.434 2801 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.42 % Favored : 92.50 % Rotamer Outliers : 0.15 % 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: -0.73 (0.17), residues: 2561 helix: 1.54 (0.18), residues: 884 sheet: -0.87 (0.26), residues: 411 loop : -1.90 (0.18), residues: 1266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5122 Ramachandran restraints generated. 2561 Oldfield, 0 Emsley, 2561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 145 average time/residue: 0.2893 time to fit residues: 65.9753 Evaluate side-chains 147 residues out of total 2212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 2.001 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1837 time to fit residues: 3.4067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.0010 chunk 62 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 29 optimal weight: 30.0000 chunk 56 optimal weight: 0.3980 chunk 203 optimal weight: 0.0270 chunk 85 optimal weight: 20.0000 chunk 208 optimal weight: 2.9990 chunk 25 optimal weight: 50.0000 chunk 37 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.0848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.152908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.126653 restraints weight = 42369.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.120309 restraints weight = 47852.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.117957 restraints weight = 42451.578| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 17570 Z= 0.206 Angle : 0.612 13.614 24210 Z= 0.308 Chirality : 0.046 0.482 3037 Planarity : 0.004 0.073 3125 Dihedral : 9.078 109.456 2801 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.69 % Favored : 92.23 % Rotamer Outliers : 0.29 % 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: -0.70 (0.17), residues: 2561 helix: 1.59 (0.18), residues: 884 sheet: -0.95 (0.26), residues: 431 loop : -1.88 (0.18), residues: 1246 =============================================================================== Job complete usr+sys time: 3038.49 seconds wall clock time: 55 minutes 43.80 seconds (3343.80 seconds total)