Starting phenix.real_space_refine (version: dev) on Thu Feb 23 00:01:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2023/8e94_27955_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2023/8e94_27955.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2023/8e94_27955_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2023/8e94_27955_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2023/8e94_27955_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2023/8e94_27955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2023/8e94_27955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2023/8e94_27955_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2023/8e94_27955_updated.pdb" } resolution = 3.72 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= 0.010 sd= 0.740 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 GLU 277": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A ARG 695": "NH1" <-> "NH2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "C GLU 712": "OE1" <-> "OE2" Residue "D GLU 239": "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: 18816 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 4710 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 29, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 498 Unresolved non-hydrogen angles: 608 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 11, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 35, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 340 Chain: "B" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 4587 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 38, 'TRANS': 603} Chain breaks: 2 Unresolved non-hydrogen bonds: 402 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 17, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 292 Chain: "C" Number of atoms: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 4620 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 29, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 595 Unresolved non-hydrogen angles: 726 Unresolved non-hydrogen dihedrals: 496 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 16, 'TYR:plan': 3, 'ASN:plan1': 15, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 31, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 394 Chain: "D" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4512 Classifications: {'peptide': 638} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 39, 'TRANS': 598} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 547 Unresolved non-hydrogen dihedrals: 367 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 310 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 4 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'IWB': 1} Classifications: {'undetermined': 1} Chain: "C" 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: "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: 10.83, per 1000 atoms: 0.58 Number of scatterers: 18816 At special positions: 0 Unit cell: (131.824, 147.232, 134.392, 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 80 16.00 O 3467 8.00 N 3235 7.00 C 12034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=1.90 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=2.05 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.03 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=1.88 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 Atom "HETATM18684 O5 NAG A 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM18469 O5 NAG F 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " BMA F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A 902 " - " ASN A 276 " " NAG A 903 " - " ASN A 771 " " NAG C 901 " - " ASN C 350 " " NAG C 902 " - " ASN C 203 " " NAG C 903 " - " ASN C 368 " " NAG D 901 " - " ASN D 337 " " NAG E 1 " - " ASN A 61 " " NAG F 1 " - " ASN A 368 " " NAG G 1 " - " ASN B 685 " " NAG H 1 " - " ASN B 337 " " NAG I 1 " - " ASN C 276 " " NAG J 1 " - " ASN C 61 " " NAG K 1 " - " ASN C 771 " Time building additional restraints: 7.94 Conformation dependent library (CDL) restraints added in 3.0 seconds 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4798 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 28 sheets defined 31.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 38 through 52 removed outlier: 3.541A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.636A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.796A pdb=" N GLN A 147 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 158 " --> pdb=" O MET A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 186 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 279 through 297 removed outlier: 3.968A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 500 through 507 removed outlier: 3.828A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 526 removed outlier: 4.077A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 673 No H-bonds generated for 'chain 'A' and resid 670 through 673' Processing helix chain 'A' and resid 688 through 694 Processing helix chain 'A' and resid 697 through 708 removed outlier: 5.840A pdb=" N THR A 701 " --> pdb=" O GLU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.546A pdb=" N GLU A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 784 through 793 Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 74 through 88 Processing helix chain 'B' and resid 105 through 115 Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.921A pdb=" N ARG B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 217 Processing helix chain 'B' and resid 230 through 242 removed outlier: 4.134A pdb=" N GLU B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 306 removed outlier: 4.043A pdb=" N GLN B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 removed outlier: 3.778A pdb=" N TYR B 332 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 666 through 669 No H-bonds generated for 'chain 'B' and resid 666 through 669' Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'B' and resid 711 through 720 removed outlier: 3.621A pdb=" N THR B 716 " --> pdb=" O GLU B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 738 Processing helix chain 'B' and resid 769 through 783 removed outlier: 3.533A pdb=" N ASP B 774 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 793 removed outlier: 3.806A pdb=" N LEU B 789 " --> pdb=" O GLU B 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 52 Processing helix chain 'C' and resid 71 through 83 Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 144 through 157 Processing helix chain 'C' and resid 171 through 187 removed outlier: 4.214A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 225 through 237 removed outlier: 4.231A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 258 through 261 No H-bonds generated for 'chain 'C' and resid 258 through 261' Processing helix chain 'C' and resid 279 through 298 removed outlier: 4.383A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'C' and resid 458 through 470 removed outlier: 3.701A pdb=" N THR C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 521 through 524 No H-bonds generated for 'chain 'C' and resid 521 through 524' Processing helix chain 'C' and resid 670 through 673 No H-bonds generated for 'chain 'C' and resid 670 through 673' Processing helix chain 'C' and resid 688 through 695 Processing helix chain 'C' and resid 698 through 708 removed outlier: 4.513A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 722 Processing helix chain 'C' and resid 733 through 742 Processing helix chain 'C' and resid 768 through 782 removed outlier: 3.846A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 792 Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 105 through 115 Processing helix chain 'D' and resid 146 through 160 removed outlier: 3.926A pdb=" N VAL D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 153 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 187 removed outlier: 3.744A pdb=" N ARG D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 285 through 304 Processing helix chain 'D' and resid 326 through 335 Processing helix chain 'D' and resid 457 through 469 Processing helix chain 'D' and resid 493 through 499 Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 666 through 669 No H-bonds generated for 'chain 'D' and resid 666 through 669' Processing helix chain 'D' and resid 687 through 695 removed outlier: 4.207A pdb=" N ASN D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 704 removed outlier: 4.087A pdb=" N VAL D 704 " --> pdb=" O HIS D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 720 Processing helix chain 'D' and resid 730 through 736 removed outlier: 3.701A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 783 removed outlier: 3.934A pdb=" N ALA D 772 " --> pdb=" O HIS D 768 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 775 " --> pdb=" O ARG D 771 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP D 783 " --> pdb=" O GLN D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 793 Processing sheet with id= A, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= B, first strand: chain 'A' and resid 193 through 197 Processing sheet with id= C, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.793A pdb=" N GLY A 268 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 397 through 402 removed outlier: 6.427A pdb=" N THR A 473 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE A 400 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU A 475 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N THR A 402 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N HIS A 477 " --> pdb=" O THR A 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 409 through 412 Processing sheet with id= F, first strand: chain 'A' and resid 534 through 537 removed outlier: 4.089A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 728 through 732 removed outlier: 4.471A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.180A pdb=" N VAL B 32 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL B 67 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 34 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 197 through 200 removed outlier: 6.749A pdb=" N VAL B 251 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA B 226 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 253 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.885A pdb=" N GLY B 373 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA B 362 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N MET B 371 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 405 through 407 removed outlier: 3.511A pdb=" N TYR B 476 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR B 407 " --> pdb=" O TYR B 476 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 414 through 417 removed outlier: 3.508A pdb=" N GLU B 417 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 453 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 531 through 535 Processing sheet with id= N, first strand: chain 'C' and resid 26 through 33 removed outlier: 6.382A pdb=" N GLN C 59 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE C 29 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN C 61 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N ALA C 31 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C 63 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU C 33 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 65 " --> pdb=" O LEU C 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 90 through 92 Processing sheet with id= P, first strand: chain 'C' and resid 194 through 197 removed outlier: 6.718A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 222 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL C 246 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N LEU C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU C 248 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 268 through 271 removed outlier: 4.227A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN C 357 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 397 through 402 removed outlier: 6.150A pdb=" N THR C 473 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE C 400 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU C 475 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR C 402 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N HIS C 477 " --> pdb=" O THR C 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 409 through 412 Processing sheet with id= T, first strand: chain 'C' and resid 486 through 489 Processing sheet with id= U, first strand: chain 'C' and resid 534 through 536 removed outlier: 4.488A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 536 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 729 through 732 removed outlier: 3.990A pdb=" N PHE C 729 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 32 through 34 removed outlier: 7.137A pdb=" N GLY D 92 " --> pdb=" O ALA D 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 197 through 201 removed outlier: 3.714A pdb=" N LEU D 201 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 274 through 277 removed outlier: 3.659A pdb=" N GLY D 373 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA D 362 " --> pdb=" O MET D 371 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N MET D 371 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 402 through 407 removed outlier: 6.782A pdb=" N SER D 472 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL D 405 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP D 474 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N THR D 407 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR D 476 " --> pdb=" O THR D 407 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 414 through 417 Processing sheet with id= AB, first strand: chain 'D' and resid 531 through 534 581 hydrogen bonds defined for protein. 1596 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: 5.45 Time building geometry restraints manager: 8.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2971 1.29 - 1.43: 5205 1.43 - 1.58: 10949 1.58 - 1.72: 0 1.72 - 1.86: 124 Bond restraints: 19249 Sorted by residual: bond pdb=" C7 IWB B 901 " pdb=" N6 IWB B 901 " ideal model delta sigma weight residual 1.585 1.331 0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C11 IWB B 901 " pdb=" C12 IWB B 901 " ideal model delta sigma weight residual 1.528 1.357 0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C24 IWB B 901 " pdb=" N6 IWB B 901 " ideal model delta sigma weight residual 1.498 1.349 0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C PRO D 388 " pdb=" O PRO D 388 " ideal model delta sigma weight residual 1.233 1.150 0.083 1.23e-02 6.61e+03 4.53e+01 bond pdb=" C PRO D 396 " pdb=" O PRO D 396 " ideal model delta sigma weight residual 1.234 1.166 0.067 1.08e-02 8.57e+03 3.88e+01 ... (remaining 19244 not shown) Histogram of bond angle deviations from ideal: 96.24 - 104.02: 359 104.02 - 111.80: 9654 111.80 - 119.58: 6580 119.58 - 127.36: 9539 127.36 - 135.14: 251 Bond angle restraints: 26383 Sorted by residual: angle pdb=" C2 NAG C 903 " pdb=" C1 NAG C 903 " pdb=" O5 NAG C 903 " ideal model delta sigma weight residual 109.64 118.58 -8.94 5.38e-01 3.45e+00 2.76e+02 angle pdb=" C2 NAG F 4 " pdb=" C1 NAG F 4 " pdb=" O5 NAG F 4 " ideal model delta sigma weight residual 109.64 114.67 -5.03 5.38e-01 3.45e+00 8.73e+01 angle pdb=" C GLY D 260 " pdb=" N SER D 261 " pdb=" CA SER D 261 " ideal model delta sigma weight residual 120.28 130.71 -10.43 1.34e+00 5.57e-01 6.06e+01 angle pdb=" CA ARG B 411 " pdb=" C ARG B 411 " pdb=" N PRO B 412 " ideal model delta sigma weight residual 120.77 128.29 -7.52 9.70e-01 1.06e+00 6.01e+01 angle pdb=" C PRO D 396 " pdb=" CA PRO D 396 " pdb=" CB PRO D 396 " ideal model delta sigma weight residual 110.85 100.12 10.73 1.41e+00 5.03e-01 5.79e+01 ... (remaining 26378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.53: 10259 20.53 - 41.06: 837 41.06 - 61.59: 129 61.59 - 82.12: 12 82.12 - 102.65: 4 Dihedral angle restraints: 11241 sinusoidal: 3790 harmonic: 7451 Sorted by residual: dihedral pdb=" C ARG B 411 " pdb=" N ARG B 411 " pdb=" CA ARG B 411 " pdb=" CB ARG B 411 " ideal model delta harmonic sigma weight residual -122.60 -150.21 27.61 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" N ARG B 411 " pdb=" C ARG B 411 " pdb=" CA ARG B 411 " pdb=" CB ARG B 411 " ideal model delta harmonic sigma weight residual 122.80 149.13 -26.33 0 2.50e+00 1.60e-01 1.11e+02 dihedral pdb=" CB CYS C 420 " pdb=" SG CYS C 420 " pdb=" SG CYS C 454 " pdb=" CB CYS C 454 " ideal model delta sinusoidal sigma weight residual 93.00 28.63 64.37 1 1.00e+01 1.00e-02 5.45e+01 ... (remaining 11238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.817: 3213 0.817 - 1.635: 3 1.635 - 2.452: 0 2.452 - 3.269: 1 3.269 - 4.086: 1 Chirality restraints: 3218 Sorted by residual: chirality pdb=" C1 NAG F 4 " pdb=" O4 BMA F 3 " pdb=" C2 NAG F 4 " pdb=" O5 NAG F 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-02 2.50e+03 3.09e+03 chirality pdb=" C7 IWB B 901 " pdb=" C18 IWB B 901 " pdb=" C8 IWB B 901 " pdb=" N6 IWB B 901 " both_signs ideal model delta sigma weight residual False -2.70 1.38 -4.09 2.00e-01 2.50e+01 4.17e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-02 2.50e+03 3.14e+02 ... (remaining 3215 not shown) Planarity restraints: 3354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 4 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG F 4 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG F 4 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG F 4 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG F 4 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.318 2.00e-02 2.50e+03 2.76e-01 9.54e+02 pdb=" C7 NAG J 1 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.485 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " 0.322 2.00e-02 2.50e+03 2.74e-01 9.36e+02 pdb=" C7 NAG A 901 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " -0.478 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " 0.054 2.00e-02 2.50e+03 ... (remaining 3351 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 19 2.23 - 2.89: 7762 2.89 - 3.56: 24962 3.56 - 4.23: 37042 4.23 - 4.90: 64272 Nonbonded interactions: 134057 Sorted by model distance: nonbonded pdb=" NE1 TRP D 304 " pdb=" O GLY D 308 " model vdw 1.557 2.520 nonbonded pdb=" ND2 ASN A 350 " pdb=" O5 NAG A 901 " model vdw 1.761 2.520 nonbonded pdb=" OD1 ASP B 97 " pdb=" N ASN B 98 " model vdw 1.845 2.520 nonbonded pdb=" NE1 TRP D 304 " pdb=" C GLY D 308 " model vdw 1.968 3.350 nonbonded pdb=" CD1 ILE A 220 " pdb=" CD1 LEU A 248 " model vdw 1.992 3.880 ... (remaining 134052 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 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 45 and (n \ ame N or name CA or name C or name O or name CB )) or resid 46 or (resid 47 thro \ ugh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thro \ ugh 55 or (resid 56 through 57 and (name N or name CA or name C or name O or nam \ e CB )) or resid 58 through 82 or (resid 83 and (name N or name CA or name C or \ name O or name CB )) or resid 84 through 98 or (resid 99 through 100 and (name N \ or name CA or name C or name O or name CB )) or resid 101 through 129 or (resid \ 130 through 131 and (name N or name CA or name C or name O or name CB )) or res \ id 132 through 158 or (resid 159 and (name N or name CA or name C or name O or n \ ame CB )) or resid 160 through 192 or (resid 193 and (name N or name CA or name \ C or name O or name CB )) or resid 194 through 211 or (resid 212 through 213 and \ (name N or name CA or name C or name O or name CB )) or resid 214 through 236 o \ r (resid 237 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 38 through 239 or (resid 240 and (name N or name CA or name C or name O or name \ CB )) or resid 241 through 250 or (resid 251 through 253 and (name N or name CA \ or name C or name O or name CB )) or resid 254 through 272 or (resid 273 and (na \ me N or name CA or name C or name O or name CB )) or resid 274 through 292 or (r \ esid 293 through 294 and (name N or name CA or name C or name O or name CB )) or \ resid 295 through 305 or (resid 306 and (name N or name CA or name C or name O \ or name CB )) or resid 307 through 322 or (resid 323 and (name N or name CA or n \ ame C or name O or name CB )) or resid 324 through 325 or (resid 326 and (name N \ or name CA or name C or name O or name CB )) or resid 327 through 342 or (resid \ 343 and (name N or name CA or name C or name O or name CB )) or (resid 344 thro \ ugh 347 and (name N or name CA or name C or name O or name CB )) or resid 348 th \ rough 359 or (resid 360 and (name N or name CA or name C or name O or name CB )) \ or resid 361 through 370 or (resid 371 and (name N or name CA or name C or name \ O or name CB )) or resid 372 through 376 or (resid 377 through 379 and (name N \ or name CA or name C or name O or name CB )) or resid 380 through 387 or (resid \ 388 and (name N or name CA or name C or name O or name CB )) or resid 389 or (re \ sid 390 and (name N or name CA or name C or name O or name CB )) or resid 391 th \ rough 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 441 or (resid \ 442 through 443 and (name N or name CA or name C or name O or name CB )) or resi \ d 444 through 445 or (resid 446 and (name N or name CA or name C or name O or na \ me CB )) or resid 447 through 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 672 or (resid 673 thro \ ugh 674 and (name N or name CA or name C or name O or name CB )) or resid 675 th \ rough 678 or (resid 679 and (name N or name CA or name 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 o \ r name C or name O or name CB )) or resid 686 through 693 or (resid 694 and (nam \ e N or name CA or name C or name O or name CB )) or resid 695 through 702 or (re \ sid 703 through 704 and (name N or name CA or name C or name O or name CB )) or \ resid 705 through 718 or (resid 719 through 721 and (name N or name CA or name C \ or name O or name CB )) or resid 722 through 723 or (resid 724 through 728 and \ (name N or name CA or name C or name O or name CB )) or resid 729 through 751 or \ (resid 752 and (name N or name CA or name C or name O or name CB )) or resid 75 \ 3 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 47 or (resid 48 through 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 155 or (resid 156 and ( \ name N or name CA or name C or name O or name CB )) or resid 157 through 177 or \ (resid 178 and (name N or name CA or name C or name O or name CB )) or resid 179 \ through 189 or (resid 190 through 193 and (name N or name CA or name C or name \ O or name CB )) or resid 194 through 214 or (resid 215 through 216 and (name N o \ r name CA or name C or name O or name CB )) or resid 217 through 224 or (resid 2 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 226 through \ 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) or r \ esid 261 through 271 or (resid 272 through 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 289 or (resid 290 through 291 and ( \ name N or name CA or name C or name O or name CB )) or resid 292 through 296 or \ (resid 297 through 303 and (name N or name CA or name C or name O or name CB )) \ or resid 304 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 and (name N or name CA or name C or n \ ame O or name CB )) or resid 340 or (resid 341 through 343 and (name N or name C \ A or name C or name O or name CB )) or (resid 344 through 347 and (name N or nam \ e CA or name C or name O or name CB )) or resid 348 through 366 or (resid 367 an \ d (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 name O or name CB )) or resid \ 380 through 425 or (resid 426 through 427 and (name N or name CA or name C or na \ me O or name CB )) or resid 428 through 503 or (resid 504 and (name N or name CA \ or name C or name O or name CB )) or resid 505 through 519 or (resid 520 and (n \ ame N or name CA 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 nam \ e O or name CB )) or resid 670 through 696 or (resid 697 through 699 and (name N \ or name CA or name C or name O or name CB )) or resid 700 through 701 or (resid \ 702 through 704 and (name N or name CA or name C or name O or name CB )) or res \ id 705 through 741 or (resid 742 through 743 and (name N or name CA or name C or \ name O or name CB )) or resid 744 through 786 or (resid 787 and (name N or name \ CA or name C or name O or name CB )) or resid 788 through 797 or resid 901 thro \ ugh 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 72 or (resid 73 and (na \ me N or name CA or name C or name O or name CB )) or resid 74 through 88 or (res \ id 89 and (name N or name CA or name C or name O or name CB )) or resid 90 throu \ gh 96 or (resid 97 through 103 and (name N or name CA or name C or name O or nam \ e CB )) or resid 104 through 132 or (resid 133 through 134 and (name N or name C \ A or name C or name O or name CB )) or resid 135 through 157 or (resid 158 and ( \ name N or name CA or name C or name O or name CB )) or resid 159 through 160 or \ (resid 161 and (name N or name CA or name C or name O or name CB )) or resid 162 \ through 179 or (resid 180 and (name N or name CA or name C or name O or name CB \ )) or resid 181 through 182 or (resid 183 through 184 and (name N or name CA or \ name C or name O or name CB )) or resid 185 through 186 or (resid 187 through 1 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 189 or (res \ id 190 and (name N or name CA or name C or name O or name CB )) or resid 191 thr \ ough 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) \ or resid 204 through 216 or (resid 217 and (name N or name CA or name C or name \ O or name CB )) or resid 218 through 219 or (resid 220 through 221 and (name N o \ r name CA or name C or name O or name CB )) or resid 222 through 231 or (resid 2 \ 32 through 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 241 or (resid 242 through 243 and (name N or name CA or name C or n \ ame O or name CB )) or resid 244 through 256 or (resid 257 through 258 and (name \ N or name CA or name C or name O or name CB )) or resid 259 through 281 or (res \ id 282 and (name N or name CA or name C or name O or name CB )) or resid 283 thr \ ough 284 or (resid 285 through 287 and (name N or name CA or name C or name O or \ name CB )) or resid 288 through 305 or (resid 306 through 307 and (name N or na \ me CA or name C or name O or name CB )) or resid 308 through 327 or (resid 328 t \ hrough 330 and (name N or name CA or name C or name O or name CB )) or resid 331 \ through 343 or (resid 344 and (name N or name CA or name C or name O or name CB \ )) or resid 345 through 363 or (resid 364 through 365 and (name N or name CA or \ name C or name O or name CB )) or resid 366 through 408 or (resid 409 through 4 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 411 through \ 416 or (resid 417 and (name N or name CA or name C or name O or name CB )) or r \ esid 418 through 435 or (resid 436 and (name N or name CA or name C or name O or \ name CB )) or resid 437 or (resid 447 through 449 and (name N or name CA or nam \ e C or name O or name CB )) or resid 450 or (resid 451 and (name N or name CA or \ name C or name O or name CB )) or resid 452 through 481 or (resid 482 and (name \ N or name CA or name C or name O or name CB )) or resid 483 through 496 or (res \ id 497 and (name N or name CA or name C or name O or name CB )) or resid 498 thr \ ough 500 or (resid 501 and (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 name C or name O or name CB )) or resid 671 through 696 or \ (resid 697 and (name N or name CA or name C or name O or name CB )) or resid 69 \ 8 or (resid 699 through 700 and (name N or name CA or name C or name O or name C \ B )) or resid 701 or (resid 702 through 703 and (name N or name CA or name C or \ name O or name CB )) or resid 704 through 705 or (resid 706 through 709 and (nam \ e N or name CA or name C or name O or name CB )) or resid 710 through 723 or (re \ sid 724 through 725 and (name N or name CA or name C or name O or name CB )) or \ resid 726 through 773 or (resid 774 and (name N or name CA or name C or name O o \ r name CB )) or resid 775 through 798)) selection = (chain 'D' and (resid 31 through 54 or (resid 55 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 262 or (resid 263 throu \ gh 264 and (name N or name CA or name C or name O or name CB )) or resid 265 thr \ ough 278 or (resid 279 and (name N or name CA or name C or name O or name CB )) \ or resid 280 through 285 or (resid 286 through 287 and (name N or name CA or nam \ e C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N o \ r name CA or name C or name O or name CB )) or resid 299 through 304 or (resid 3 \ 05 through 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 through 364 or (resid 365 and (name N or name CA or name C or name O or nam \ e CB )) or resid 366 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 or (resid 376 and (name N or name CA or nam \ e C or name O or name CB )) or resid 377 through 389 or (resid 390 and (name N o \ r name CA or name C or name O or name CB )) or resid 391 or (resid 399 and (name \ N or name CA or name C or name O or name CB )) or resid 400 through 433 or (res \ id 434 and (name N or name CA or name C or name O or name CB )) or resid 435 thr \ ough 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 (resid 455 and (name N or name CA or name C or name \ O or name CB )) or resid 456 through 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 664 or (res \ id 665 through 670 and (name N or name CA or name C or name O or name CB )) or r \ esid 671 through 672 or (resid 673 through 675 and (name N or name CA or name C \ or name O or name CB )) or resid 676 through 679 or (resid 680 and (name N or na \ me CA or name C or name O or name CB )) or resid 681 through 712 or (resid 713 t \ hrough 714 and (name N or name CA or name C or name O or name CB )) or resid 715 \ through 796 or (resid 797 and (name N or name CA or name C or name O or name CB \ )) or resid 798)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'J' } 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 80 5.16 5 C 12034 2.51 5 N 3235 2.21 5 O 3467 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: 3.200 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: 15.360 Check model and map are aligned: 0.270 Process input model: 48.350 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.180 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.006 0.254 19249 Z= 0.364 Angle : 0.910 17.684 26383 Z= 0.570 Chirality : 0.110 4.086 3218 Planarity : 0.016 0.304 3341 Dihedral : 14.911 102.654 6407 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.48 % Favored : 91.32 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.16), residues: 2570 helix: -0.07 (0.18), residues: 829 sheet: -2.09 (0.24), residues: 411 loop : -2.76 (0.16), residues: 1330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 185 average time/residue: 0.2725 time to fit residues: 81.1941 Evaluate side-chains 172 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 2.344 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2026 time to fit residues: 6.7718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 201 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS A 239 ASN A 705 HIS A 709 HIS D 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 19249 Z= 0.253 Angle : 0.652 9.557 26383 Z= 0.343 Chirality : 0.048 0.554 3218 Planarity : 0.005 0.070 3341 Dihedral : 6.311 103.152 2919 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.72 % Favored : 91.25 % Rotamer Outliers : 4.03 % 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: -2.37 (0.16), residues: 2570 helix: 0.18 (0.18), residues: 844 sheet: -1.97 (0.25), residues: 383 loop : -2.71 (0.16), residues: 1343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 173 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 38 residues processed: 224 average time/residue: 0.2591 time to fit residues: 95.0320 Evaluate side-chains 197 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 1.982 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1628 time to fit residues: 14.7535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 187 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 19249 Z= 0.227 Angle : 0.611 9.867 26383 Z= 0.318 Chirality : 0.047 0.769 3218 Planarity : 0.005 0.087 3341 Dihedral : 6.104 102.037 2919 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.16), residues: 2570 helix: 0.37 (0.18), residues: 848 sheet: -1.86 (0.26), residues: 382 loop : -2.63 (0.16), residues: 1340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 183 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 33 residues processed: 239 average time/residue: 0.2590 time to fit residues: 101.7985 Evaluate side-chains 193 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 2.124 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1836 time to fit residues: 13.8254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 156 optimal weight: 0.0470 chunk 234 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 222 optimal weight: 0.0770 chunk 66 optimal weight: 30.0000 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 19249 Z= 0.164 Angle : 0.574 9.939 26383 Z= 0.296 Chirality : 0.046 0.656 3218 Planarity : 0.004 0.072 3341 Dihedral : 5.796 101.784 2919 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer Outliers : 2.65 % 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: -1.89 (0.16), residues: 2570 helix: 0.63 (0.18), residues: 849 sheet: -1.62 (0.26), residues: 385 loop : -2.50 (0.16), residues: 1336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 190 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 24 residues processed: 224 average time/residue: 0.2643 time to fit residues: 97.3712 Evaluate side-chains 188 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 2.318 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1944 time to fit residues: 11.2794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 222 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN B 513 ASN D 366 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 19249 Z= 0.196 Angle : 0.584 11.363 26383 Z= 0.300 Chirality : 0.046 0.596 3218 Planarity : 0.004 0.070 3341 Dihedral : 5.771 102.167 2919 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.17), residues: 2570 helix: 0.64 (0.18), residues: 851 sheet: -1.58 (0.26), residues: 373 loop : -2.40 (0.16), residues: 1346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 184 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 24 residues processed: 216 average time/residue: 0.2729 time to fit residues: 98.5650 Evaluate side-chains 197 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 2.110 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1659 time to fit residues: 10.3556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 49 optimal weight: 0.3980 chunk 145 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 19249 Z= 0.207 Angle : 0.583 11.461 26383 Z= 0.301 Chirality : 0.046 0.573 3218 Planarity : 0.004 0.071 3341 Dihedral : 5.763 102.198 2919 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 1.67 % 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: -1.75 (0.17), residues: 2570 helix: 0.67 (0.18), residues: 849 sheet: -1.57 (0.26), residues: 375 loop : -2.36 (0.16), residues: 1346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 194 average time/residue: 0.2649 time to fit residues: 84.7508 Evaluate side-chains 183 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 2.223 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1621 time to fit residues: 8.9854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 181 optimal weight: 0.0060 chunk 140 optimal weight: 0.0670 chunk 209 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 overall best weight: 3.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 19249 Z= 0.265 Angle : 0.618 11.837 26383 Z= 0.318 Chirality : 0.047 0.564 3218 Planarity : 0.004 0.072 3341 Dihedral : 5.911 102.761 2919 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer Outliers : 2.19 % 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: -1.86 (0.17), residues: 2570 helix: 0.54 (0.18), residues: 852 sheet: -1.74 (0.26), residues: 383 loop : -2.35 (0.16), residues: 1335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 24 residues processed: 196 average time/residue: 0.2780 time to fit residues: 89.1893 Evaluate side-chains 186 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 2.214 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1792 time to fit residues: 11.5304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 157 optimal weight: 0.0270 chunk 168 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 23 optimal weight: 0.0670 chunk 194 optimal weight: 10.0000 overall best weight: 1.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 19249 Z= 0.188 Angle : 0.585 12.619 26383 Z= 0.299 Chirality : 0.046 0.544 3218 Planarity : 0.004 0.070 3341 Dihedral : 5.753 102.318 2919 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer Outliers : 1.09 % 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: -1.75 (0.17), residues: 2570 helix: 0.66 (0.18), residues: 857 sheet: -1.66 (0.26), residues: 376 loop : -2.33 (0.16), residues: 1337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 173 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 188 average time/residue: 0.2742 time to fit residues: 85.0940 Evaluate side-chains 173 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 2.259 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1679 time to fit residues: 5.7768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 7.9990 chunk 237 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 230 optimal weight: 0.0170 chunk 138 optimal weight: 7.9990 chunk 100 optimal weight: 0.0770 chunk 181 optimal weight: 4.9990 chunk 70 optimal weight: 0.0670 chunk 208 optimal weight: 0.9990 chunk 218 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS C 477 HIS D 141 GLN D 483 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.063 19249 Z= 0.149 Angle : 0.566 12.155 26383 Z= 0.286 Chirality : 0.045 0.520 3218 Planarity : 0.004 0.070 3341 Dihedral : 5.436 101.345 2919 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2570 helix: 0.86 (0.18), residues: 855 sheet: -1.37 (0.26), residues: 395 loop : -2.25 (0.17), residues: 1320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 200 average time/residue: 0.2692 time to fit residues: 88.8120 Evaluate side-chains 173 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 2.264 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1891 time to fit residues: 5.0572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 244 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 256 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 157 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 19249 Z= 0.278 Angle : 0.624 11.932 26383 Z= 0.320 Chirality : 0.047 0.541 3218 Planarity : 0.005 0.100 3341 Dihedral : 5.752 102.685 2919 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer Outliers : 0.52 % 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: -1.66 (0.17), residues: 2570 helix: 0.70 (0.18), residues: 857 sheet: -1.57 (0.26), residues: 398 loop : -2.25 (0.17), residues: 1315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 169 average time/residue: 0.2700 time to fit residues: 76.0193 Evaluate side-chains 168 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 2.048 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1763 time to fit residues: 4.8868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 0.0070 chunk 62 optimal weight: 0.0870 chunk 187 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107119 restraints weight = 42197.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109074 restraints weight = 26702.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110437 restraints weight = 19884.362| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 19249 Z= 0.203 Angle : 0.592 12.309 26383 Z= 0.300 Chirality : 0.046 0.526 3218 Planarity : 0.004 0.098 3341 Dihedral : 5.656 102.424 2919 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % 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: -1.58 (0.17), residues: 2570 helix: 0.77 (0.18), residues: 856 sheet: -1.53 (0.26), residues: 389 loop : -2.21 (0.17), residues: 1325 =============================================================================== Job complete usr+sys time: 3204.23 seconds wall clock time: 59 minutes 14.23 seconds (3554.23 seconds total)