Starting phenix.real_space_refine on Sun Aug 24 09:15:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8saq_40275/08_2025/8saq_40275_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8saq_40275/08_2025/8saq_40275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8saq_40275/08_2025/8saq_40275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8saq_40275/08_2025/8saq_40275.map" model { file = "/net/cci-nas-00/data/ceres_data/8saq_40275/08_2025/8saq_40275_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8saq_40275/08_2025/8saq_40275_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 11892 2.51 5 N 3201 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18946 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3367 Classifications: {'peptide': 426} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 402} Chain breaks: 4 Chain: "B" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1008 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 796 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3367 Classifications: {'peptide': 426} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 402} Chain breaks: 4 Chain: "F" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1008 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "I" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 796 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "K" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3379 Classifications: {'peptide': 428} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "L" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 991 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "M" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "N" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 796 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} 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: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.38, per 1000 atoms: 0.28 Number of scatterers: 18946 At special positions: 0 Unit cell: (155.636, 155.636, 137.514, 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 142 16.00 O 3711 8.00 N 3201 7.00 C 11892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 581 " distance=2.04 Simple disulfide: pdb=" SG CYS B 574 " - pdb=" SG CYS B 580 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 541 " - pdb=" SG CYS D 626 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS I 320 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 207 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 159 " distance=2.03 Simple disulfide: pdb=" SG CYS K 220 " - pdb=" SG CYS K 249 " distance=2.05 Simple disulfide: pdb=" SG CYS K 230 " - pdb=" SG CYS K 241 " distance=2.03 Simple disulfide: pdb=" SG CYS K 298 " - pdb=" SG CYS K 333 " distance=2.03 Simple disulfide: pdb=" SG CYS K 380 " - pdb=" SG CYS K 447 " distance=2.03 Simple disulfide: pdb=" SG CYS K 387 " - pdb=" SG CYS K 420 " distance=2.03 Simple disulfide: pdb=" SG CYS K 503 " - pdb=" SG CYS L 607 " distance=2.04 Simple disulfide: pdb=" SG CYS L 600 " - pdb=" SG CYS L 606 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 252 " - pdb=" SG CYS N 320 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " BMA R 3 " - " MAN R 7 " " BMA V 3 " - " MAN V 7 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A 601 " - " ASN A 156 " " NAG A 602 " - " ASN A 442 " " NAG E 601 " - " ASN E 156 " " NAG E 602 " - " ASN E 442 " " NAG G 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG K 601 " - " ASN K 158 " " NAG K 602 " - " ASN K 444 " " NAG Q 1 " - " ASN E 301 " " NAG R 1 " - " ASN E 332 " " NAG U 1 " - " ASN K 303 " " NAG V 1 " - " ASN K 334 " Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 835.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4360 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 44 sheets defined 21.4% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 353 removed outlier: 4.147A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.615A pdb=" N GLY A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 381' Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.960A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'B' and resid 514 through 519 Processing helix chain 'B' and resid 545 through 572 removed outlier: 4.104A pdb=" N ILE B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA B 554 " --> pdb=" O LYS B 550 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 591 Processing helix chain 'B' and resid 597 through 602 removed outlier: 3.836A pdb=" N MET B 602 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 612 Processing helix chain 'B' and resid 614 through 639 removed outlier: 3.776A pdb=" N GLU B 624 " --> pdb=" O GLY B 620 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 629 " --> pdb=" O SER B 625 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASN B 632 " --> pdb=" O GLN B 628 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 617 through 621 Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.095A pdb=" N THR E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 350 removed outlier: 3.587A pdb=" N GLN E 350 " --> pdb=" O GLY E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 538 through 543 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.898A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 621 through 626 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 650 removed outlier: 3.653A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 662 removed outlier: 4.037A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.565A pdb=" N GLN H 65 " --> pdb=" O ARG H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 257 through 262 removed outlier: 4.775A pdb=" N HIS I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 315 Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 99 through 117 Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'K' and resid 197 through 200 Processing helix chain 'K' and resid 336 through 356 removed outlier: 4.028A pdb=" N LYS K 353 " --> pdb=" O LYS K 349 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS K 354 " --> pdb=" O GLU K 350 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE K 356 " --> pdb=" O LEU K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 375 Processing helix chain 'K' and resid 477 through 483 removed outlier: 3.904A pdb=" N TRP K 481 " --> pdb=" O MET K 477 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER K 483 " --> pdb=" O ASP K 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 536 Processing helix chain 'L' and resid 540 through 545 removed outlier: 3.642A pdb=" N ASN L 545 " --> pdb=" O VAL L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 598 removed outlier: 3.742A pdb=" N ILE L 575 " --> pdb=" O THR L 571 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA L 580 " --> pdb=" O LYS L 576 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP L 598 " --> pdb=" O LEU L 594 " (cutoff:3.500A) Processing helix chain 'L' and resid 613 through 617 Processing helix chain 'L' and resid 623 through 627 removed outlier: 3.685A pdb=" N ASN L 627 " --> pdb=" O ILE L 624 " (cutoff:3.500A) Processing helix chain 'L' and resid 629 through 638 Processing helix chain 'L' and resid 640 through 662 removed outlier: 3.750A pdb=" N ILE L 644 " --> pdb=" O TYR L 640 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU L 650 " --> pdb=" O GLY L 646 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN L 653 " --> pdb=" O GLU L 649 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN L 655 " --> pdb=" O SER L 651 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 311 through 315 removed outlier: 3.540A pdb=" N GLU N 315 " --> pdb=" O ALA N 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.218A pdb=" N VAL B 584 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL A 38 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR B 582 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR A 40 " --> pdb=" O CYS B 580 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N CYS B 580 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.815A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.621A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.994A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.904A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.273A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.458A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.295A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.354A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.779A pdb=" N ARG A 273 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 11.354A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.295A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.458A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.273A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.904A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 361 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.070A pdb=" N LYS C 12 " --> pdb=" O THR C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 18 through 22 removed outlier: 3.651A pdb=" N VAL C 18 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 51 removed outlier: 6.765A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 528 through 531 removed outlier: 3.570A pdb=" N ALA D 622 " --> pdb=" O VAL D 643 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 528 through 531 removed outlier: 3.570A pdb=" N ALA D 622 " --> pdb=" O VAL D 643 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 536 through 542 Processing sheet with id=AB7, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.380A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.517A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.730A pdb=" N CYS E 218 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.934A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.739A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.792A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.784A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.158A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.639A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.639A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.158A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.784A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR E 361 " --> pdb=" O GLY E 393 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY E 393 " --> pdb=" O TYR E 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AC7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.889A pdb=" N LYS H 12 " --> pdb=" O THR H 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 21 through 22 Processing sheet with id=AC9, first strand: chain 'H' and resid 45 through 51 removed outlier: 5.354A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR H 94 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR H 121 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 239 through 242 removed outlier: 3.595A pdb=" N ALA I 316 " --> pdb=" O VAL I 337 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 239 through 242 removed outlier: 3.595A pdb=" N ALA I 316 " --> pdb=" O VAL I 337 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 248 through 250 Processing sheet with id=AD4, first strand: chain 'K' and resid 496 through 501 removed outlier: 5.415A pdb=" N VAL L 610 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL K 38 " --> pdb=" O THR L 608 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR L 608 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N TYR K 40 " --> pdb=" O CYS L 606 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N CYS L 606 " --> pdb=" O TYR K 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 45 through 47 removed outlier: 3.629A pdb=" N ILE K 227 " --> pdb=" O VAL K 247 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 92 through 93 removed outlier: 3.878A pdb=" N PHE K 93 " --> pdb=" O GLY K 239 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY K 239 " --> pdb=" O PHE K 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'K' and resid 171 through 179 removed outlier: 3.697A pdb=" N ASN K 158 " --> pdb=" O SER K 132 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 261 through 263 removed outlier: 3.972A pdb=" N GLY K 453 " --> pdb=" O LEU K 262 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N THR K 446 " --> pdb=" O ILE K 296 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE K 296 " --> pdb=" O THR K 446 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N LYS K 448 " --> pdb=" O VAL K 294 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N VAL K 294 " --> pdb=" O LYS K 448 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N ASN K 450 " --> pdb=" O THR K 292 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N THR K 292 " --> pdb=" O ASN K 450 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N THR K 452 " --> pdb=" O LEU K 290 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE K 384 " --> pdb=" O LYS K 423 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 273 through 275 removed outlier: 7.286A pdb=" N THR K 452 " --> pdb=" O LEU K 290 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N THR K 292 " --> pdb=" O ASN K 450 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N ASN K 450 " --> pdb=" O THR K 292 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N VAL K 294 " --> pdb=" O LYS K 448 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N LYS K 448 " --> pdb=" O VAL K 294 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE K 296 " --> pdb=" O THR K 446 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N THR K 446 " --> pdb=" O ILE K 296 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS K 362 " --> pdb=" O PHE K 470 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR K 363 " --> pdb=" O GLY K 412 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY K 412 " --> pdb=" O TYR K 363 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 306 through 313 removed outlier: 4.085A pdb=" N GLN K 317 " --> pdb=" O ILE K 313 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 425 through 426 Processing sheet with id=AE3, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.198A pdb=" N THR M 124 " --> pdb=" O GLN M 10 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS M 12 " --> pdb=" O THR M 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'M' and resid 19 through 22 removed outlier: 3.521A pdb=" N CYS M 22 " --> pdb=" O ALA M 79 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA M 79 " --> pdb=" O CYS M 22 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 46 through 51 removed outlier: 5.582A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 239 through 242 removed outlier: 3.782A pdb=" N THR N 338 " --> pdb=" O VAL N 240 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA N 316 " --> pdb=" O VAL N 337 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 239 through 242 removed outlier: 3.782A pdb=" N THR N 338 " --> pdb=" O VAL N 240 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA N 316 " --> pdb=" O VAL N 337 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 248 through 250 610 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.84 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6147 1.36 - 1.50: 5381 1.50 - 1.65: 7623 1.65 - 1.79: 17 1.79 - 1.93: 177 Bond restraints: 19345 Sorted by residual: bond pdb=" CB CYS K 220 " pdb=" SG CYS K 220 " ideal model delta sigma weight residual 1.808 1.927 -0.119 3.30e-02 9.18e+02 1.30e+01 bond pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " ideal model delta sigma weight residual 1.808 1.919 -0.111 3.30e-02 9.18e+02 1.14e+01 bond pdb=" N GLY F 521 " pdb=" CA GLY F 521 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.46e+00 bond pdb=" N GLY B 497 " pdb=" CA GLY B 497 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.15e+00 bond pdb=" C2 MAN R 5 " pdb=" O2 MAN R 5 " ideal model delta sigma weight residual 1.407 1.452 -0.045 2.00e-02 2.50e+03 5.05e+00 ... (remaining 19340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 25960 3.54 - 7.08: 275 7.08 - 10.62: 13 10.62 - 14.16: 2 14.16 - 17.70: 3 Bond angle restraints: 26253 Sorted by residual: angle pdb=" C VAL E 120 " pdb=" N LYS E 121 " pdb=" CA LYS E 121 " ideal model delta sigma weight residual 121.70 139.40 -17.70 1.80e+00 3.09e-01 9.67e+01 angle pdb=" C VAL K 120 " pdb=" N LYS K 121 " pdb=" CA LYS K 121 " ideal model delta sigma weight residual 121.70 138.38 -16.68 1.80e+00 3.09e-01 8.59e+01 angle pdb=" C VAL A 120 " pdb=" N LYS A 121 " pdb=" CA LYS A 121 " ideal model delta sigma weight residual 121.70 138.32 -16.62 1.80e+00 3.09e-01 8.53e+01 angle pdb=" CA CYS K 249 " pdb=" CB CYS K 249 " pdb=" SG CYS K 249 " ideal model delta sigma weight residual 114.40 127.41 -13.01 2.30e+00 1.89e-01 3.20e+01 angle pdb=" CA CYS A 247 " pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 114.40 126.79 -12.39 2.30e+00 1.89e-01 2.90e+01 ... (remaining 26248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 11299 21.71 - 43.43: 597 43.43 - 65.14: 76 65.14 - 86.86: 49 86.86 - 108.57: 26 Dihedral angle restraints: 12047 sinusoidal: 5248 harmonic: 6799 Sorted by residual: dihedral pdb=" CB CYS K 220 " pdb=" SG CYS K 220 " pdb=" SG CYS K 249 " pdb=" CB CYS K 249 " ideal model delta sinusoidal sigma weight residual 93.00 25.25 67.75 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 96 " pdb=" CB CYS M 96 " ideal model delta sinusoidal sigma weight residual 93.00 32.38 60.62 1 1.00e+01 1.00e-02 4.89e+01 dihedral pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual 93.00 34.18 58.82 1 1.00e+01 1.00e-02 4.63e+01 ... (remaining 12044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2411 0.057 - 0.114: 449 0.114 - 0.171: 153 0.171 - 0.228: 9 0.228 - 0.285: 6 Chirality restraints: 3028 Sorted by residual: chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 3025 not shown) Planarity restraints: 3301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 456 " 0.286 9.50e-02 1.11e+02 1.28e-01 1.09e+01 pdb=" NE ARG E 456 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG E 456 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 456 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 456 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 287 " 0.009 2.00e-02 2.50e+03 2.16e-02 7.00e+00 pdb=" CG HIS A 287 " -0.040 2.00e-02 2.50e+03 pdb=" ND1 HIS A 287 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS A 287 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS A 287 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS A 287 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 532 " 0.045 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO D 533 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 533 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 533 " 0.037 5.00e-02 4.00e+02 ... (remaining 3298 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 163 2.57 - 3.15: 15648 3.15 - 3.73: 26560 3.73 - 4.32: 37553 4.32 - 4.90: 63650 Nonbonded interactions: 143574 Sorted by model distance: nonbonded pdb=" O PRO N 237 " pdb=" OG1 THR N 335 " model vdw 1.985 3.040 nonbonded pdb=" O MET E 369 " pdb=" OG1 THR E 373 " model vdw 2.024 3.040 nonbonded pdb=" O MET A 369 " pdb=" OG1 THR A 373 " model vdw 2.025 3.040 nonbonded pdb=" O MET K 371 " pdb=" OG1 THR K 375 " model vdw 2.041 3.040 nonbonded pdb=" OG SER N 299 " pdb=" O THR N 302 " model vdw 2.064 3.040 ... (remaining 143569 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = (chain 'K' and (resid 31 through 152 or resid 155 through 602)) } ncs_group { reference = (chain 'B' and resid 497 through 638) selection = (chain 'F' and resid 521 through 662) selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.250 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.005 0.119 19420 Z= 0.239 Angle : 0.912 17.703 26439 Z= 0.455 Chirality : 0.053 0.285 3028 Planarity : 0.006 0.128 3289 Dihedral : 14.836 108.574 7570 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.75 % Favored : 92.03 % Rotamer: Outliers : 0.05 % Allowed : 0.39 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.18), residues: 2310 helix: -0.60 (0.27), residues: 381 sheet: -1.16 (0.19), residues: 666 loop : -1.33 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 38 TYR 0.034 0.002 TYR D 546 PHE 0.032 0.002 PHE H 114 TRP 0.025 0.002 TRP A 35 HIS 0.030 0.003 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00545 (19345) covalent geometry : angle 0.88454 (26253) SS BOND : bond 0.00553 ( 39) SS BOND : angle 2.27370 ( 78) hydrogen bonds : bond 0.22498 ( 582) hydrogen bonds : angle 8.59229 ( 1635) link_ALPHA1-2 : bond 0.00762 ( 6) link_ALPHA1-2 : angle 3.52319 ( 18) link_ALPHA1-3 : bond 0.00654 ( 3) link_ALPHA1-3 : angle 3.77234 ( 9) link_ALPHA1-6 : bond 0.00685 ( 3) link_ALPHA1-6 : angle 2.05215 ( 9) link_BETA1-4 : bond 0.00853 ( 12) link_BETA1-4 : angle 3.62740 ( 36) link_NAG-ASN : bond 0.00485 ( 12) link_NAG-ASN : angle 2.12972 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.6805 (tmm) cc_final: 0.5764 (tmm) REVERT: B 519 ASN cc_start: 0.8801 (t0) cc_final: 0.8429 (t0) REVERT: B 566 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8444 (tp40) REVERT: B 577 LYS cc_start: 0.7481 (mmmt) cc_final: 0.7075 (tptp) REVERT: D 537 ILE cc_start: 0.6582 (mm) cc_final: 0.6369 (mt) REVERT: E 47 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6871 (tm-30) REVERT: E 109 ILE cc_start: 0.9330 (mm) cc_final: 0.9084 (mt) REVERT: E 280 ASN cc_start: 0.7945 (m-40) cc_final: 0.7346 (t0) REVERT: F 635 ILE cc_start: 0.8616 (mm) cc_final: 0.8310 (mm) REVERT: H 3 GLN cc_start: 0.7045 (tp-100) cc_final: 0.6813 (mp10) REVERT: H 38 ARG cc_start: 0.8626 (tmm-80) cc_final: 0.8057 (ttp80) REVERT: H 75 SER cc_start: 0.7843 (p) cc_final: 0.7294 (p) REVERT: I 298 LYS cc_start: 0.8785 (tttt) cc_final: 0.8158 (tttp) REVERT: K 219 TYR cc_start: 0.7947 (m-10) cc_final: 0.7707 (m-80) REVERT: K 428 MET cc_start: 0.5168 (tpp) cc_final: 0.4640 (tpp) REVERT: N 330 VAL cc_start: 0.8637 (m) cc_final: 0.8367 (m) outliers start: 1 outliers final: 0 residues processed: 392 average time/residue: 0.1561 time to fit residues: 92.2632 Evaluate side-chains 289 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.4980 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS E 377 ASN I 301 ASN K 72 HIS M 43 GLN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.144635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121168 restraints weight = 33059.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124134 restraints weight = 22223.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126161 restraints weight = 16911.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127535 restraints weight = 13973.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128535 restraints weight = 12227.794| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19420 Z= 0.140 Angle : 0.743 31.455 26439 Z= 0.363 Chirality : 0.047 0.267 3028 Planarity : 0.004 0.050 3289 Dihedral : 10.983 88.655 3257 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.63 % Favored : 94.16 % Rotamer: Outliers : 1.37 % Allowed : 7.42 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.18), residues: 2310 helix: 0.06 (0.27), residues: 392 sheet: -0.79 (0.20), residues: 687 loop : -1.24 (0.19), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 293 TYR 0.027 0.002 TYR E 217 PHE 0.023 0.002 PHE K 85 TRP 0.015 0.001 TRP A 35 HIS 0.006 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00311 (19345) covalent geometry : angle 0.71906 (26253) SS BOND : bond 0.00556 ( 39) SS BOND : angle 2.53546 ( 78) hydrogen bonds : bond 0.04421 ( 582) hydrogen bonds : angle 5.94590 ( 1635) link_ALPHA1-2 : bond 0.00447 ( 6) link_ALPHA1-2 : angle 2.21780 ( 18) link_ALPHA1-3 : bond 0.01454 ( 3) link_ALPHA1-3 : angle 1.00929 ( 9) link_ALPHA1-6 : bond 0.00271 ( 3) link_ALPHA1-6 : angle 1.43753 ( 9) link_BETA1-4 : bond 0.00654 ( 12) link_BETA1-4 : angle 2.46375 ( 36) link_NAG-ASN : bond 0.00480 ( 12) link_NAG-ASN : angle 2.24191 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 318 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.7932 (m-40) cc_final: 0.7654 (m-40) REVERT: A 426 MET cc_start: 0.6857 (tmm) cc_final: 0.5946 (tmm) REVERT: B 506 MET cc_start: 0.7614 (mtp) cc_final: 0.7296 (mtp) REVERT: B 519 ASN cc_start: 0.9115 (t0) cc_final: 0.8851 (t0) REVERT: B 566 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8483 (tp40) REVERT: E 109 ILE cc_start: 0.9288 (mm) cc_final: 0.9063 (mt) REVERT: E 113 ASP cc_start: 0.8133 (t0) cc_final: 0.7856 (t0) REVERT: E 115 SER cc_start: 0.8799 (t) cc_final: 0.8571 (p) REVERT: E 377 ASN cc_start: 0.7359 (OUTLIER) cc_final: 0.7073 (p0) REVERT: F 626 MET cc_start: 0.6953 (ttm) cc_final: 0.6641 (ttm) REVERT: F 634 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7460 (mt-10) REVERT: H 10 GLN cc_start: 0.7028 (mp-120) cc_final: 0.6755 (mp-120) REVERT: H 38 ARG cc_start: 0.8657 (tmm-80) cc_final: 0.7748 (ttp-170) REVERT: M 48 MET cc_start: 0.7517 (mtp) cc_final: 0.7014 (mtp) outliers start: 28 outliers final: 16 residues processed: 332 average time/residue: 0.1478 time to fit residues: 75.1018 Evaluate side-chains 297 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 280 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain N residue 338 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 133 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 203 optimal weight: 7.9990 chunk 58 optimal weight: 0.1980 chunk 198 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 174 optimal weight: 0.6980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN K 480 ASN M 6 GLN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118215 restraints weight = 33785.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121016 restraints weight = 23146.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122960 restraints weight = 17803.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124213 restraints weight = 14833.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125166 restraints weight = 13090.538| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19420 Z= 0.185 Angle : 0.753 35.807 26439 Z= 0.359 Chirality : 0.048 0.216 3028 Planarity : 0.005 0.054 3289 Dihedral : 10.020 89.448 3257 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.45 % Favored : 93.38 % Rotamer: Outliers : 1.71 % Allowed : 10.06 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.18), residues: 2310 helix: 0.17 (0.27), residues: 391 sheet: -0.78 (0.20), residues: 645 loop : -1.19 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 311 TYR 0.028 0.002 TYR I 278 PHE 0.020 0.002 PHE E 85 TRP 0.017 0.001 TRP A 35 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00430 (19345) covalent geometry : angle 0.73123 (26253) SS BOND : bond 0.00705 ( 39) SS BOND : angle 2.27283 ( 78) hydrogen bonds : bond 0.04196 ( 582) hydrogen bonds : angle 5.60170 ( 1635) link_ALPHA1-2 : bond 0.00369 ( 6) link_ALPHA1-2 : angle 2.01019 ( 18) link_ALPHA1-3 : bond 0.01121 ( 3) link_ALPHA1-3 : angle 1.28565 ( 9) link_ALPHA1-6 : bond 0.00308 ( 3) link_ALPHA1-6 : angle 1.44421 ( 9) link_BETA1-4 : bond 0.00691 ( 12) link_BETA1-4 : angle 2.37987 ( 36) link_NAG-ASN : bond 0.00509 ( 12) link_NAG-ASN : angle 2.50191 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 292 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8350 (mt) cc_final: 0.8022 (pp) REVERT: A 426 MET cc_start: 0.6924 (tmm) cc_final: 0.5883 (tmm) REVERT: B 519 ASN cc_start: 0.9194 (t0) cc_final: 0.8829 (t0) REVERT: B 566 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8458 (tp40) REVERT: C 4 LEU cc_start: 0.6806 (mm) cc_final: 0.6597 (mm) REVERT: C 10 GLN cc_start: 0.7360 (mp10) cc_final: 0.6971 (mp10) REVERT: C 48 MET cc_start: 0.7712 (mtp) cc_final: 0.7401 (mtp) REVERT: C 70 MET cc_start: 0.8151 (mtm) cc_final: 0.7895 (mtm) REVERT: E 113 ASP cc_start: 0.8251 (t0) cc_final: 0.7968 (t0) REVERT: E 115 SER cc_start: 0.8881 (t) cc_final: 0.8607 (p) REVERT: F 626 MET cc_start: 0.6863 (ttm) cc_final: 0.6267 (ttm) REVERT: F 634 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7530 (mt-10) REVERT: H 10 GLN cc_start: 0.7143 (mp-120) cc_final: 0.6730 (mp-120) REVERT: M 48 MET cc_start: 0.7664 (mtp) cc_final: 0.7294 (mtp) REVERT: N 263 ASP cc_start: 0.7761 (t0) cc_final: 0.7348 (t0) REVERT: N 270 GLN cc_start: 0.5847 (pt0) cc_final: 0.5372 (pt0) REVERT: N 319 TYR cc_start: 0.8244 (m-80) cc_final: 0.7533 (m-80) outliers start: 35 outliers final: 23 residues processed: 309 average time/residue: 0.1479 time to fit residues: 70.1675 Evaluate side-chains 287 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain N residue 338 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 161 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 22 optimal weight: 0.0370 chunk 61 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 overall best weight: 3.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS C 3 GLN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN E 66 HIS E 249 HIS E 377 ASN H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119433 restraints weight = 33188.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121738 restraints weight = 22427.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123163 restraints weight = 17079.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.123831 restraints weight = 14537.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124432 restraints weight = 13819.883| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19420 Z= 0.187 Angle : 0.752 42.349 26439 Z= 0.350 Chirality : 0.047 0.187 3028 Planarity : 0.004 0.051 3289 Dihedral : 9.318 89.424 3257 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.67 % Favored : 93.16 % Rotamer: Outliers : 2.54 % Allowed : 12.89 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.18), residues: 2310 helix: 0.24 (0.27), residues: 391 sheet: -0.79 (0.21), residues: 618 loop : -1.25 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 311 TYR 0.023 0.002 TYR I 278 PHE 0.019 0.002 PHE A 85 TRP 0.019 0.001 TRP E 35 HIS 0.008 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00435 (19345) covalent geometry : angle 0.73268 (26253) SS BOND : bond 0.00219 ( 39) SS BOND : angle 2.01640 ( 78) hydrogen bonds : bond 0.03891 ( 582) hydrogen bonds : angle 5.43583 ( 1635) link_ALPHA1-2 : bond 0.00301 ( 6) link_ALPHA1-2 : angle 1.89887 ( 18) link_ALPHA1-3 : bond 0.01186 ( 3) link_ALPHA1-3 : angle 1.37394 ( 9) link_ALPHA1-6 : bond 0.00430 ( 3) link_ALPHA1-6 : angle 1.41911 ( 9) link_BETA1-4 : bond 0.00695 ( 12) link_BETA1-4 : angle 2.28141 ( 36) link_NAG-ASN : bond 0.00482 ( 12) link_NAG-ASN : angle 2.56357 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 293 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8326 (mt) cc_final: 0.8113 (pp) REVERT: A 426 MET cc_start: 0.6972 (tmm) cc_final: 0.5871 (tmm) REVERT: A 474 ASP cc_start: 0.5571 (OUTLIER) cc_final: 0.5123 (p0) REVERT: B 506 MET cc_start: 0.7711 (mtp) cc_final: 0.7433 (mtp) REVERT: B 519 ASN cc_start: 0.9137 (t0) cc_final: 0.8930 (t0) REVERT: B 566 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8483 (tp40) REVERT: B 599 TRP cc_start: 0.8750 (m100) cc_final: 0.8308 (m100) REVERT: C 10 GLN cc_start: 0.7374 (mp10) cc_final: 0.6988 (mp-120) REVERT: C 90 ASP cc_start: 0.5667 (t70) cc_final: 0.5452 (t0) REVERT: C 111 TYR cc_start: 0.8518 (m-80) cc_final: 0.8312 (m-80) REVERT: E 113 ASP cc_start: 0.8274 (t0) cc_final: 0.8019 (t0) REVERT: E 115 SER cc_start: 0.8869 (t) cc_final: 0.8631 (p) REVERT: E 377 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7184 (p0) REVERT: F 626 MET cc_start: 0.6801 (ttm) cc_final: 0.6002 (ttm) REVERT: H 10 GLN cc_start: 0.7090 (mp-120) cc_final: 0.6706 (mp-120) REVERT: H 72 ARG cc_start: 0.6789 (pmt-80) cc_final: 0.6494 (ppt170) REVERT: H 105 TYR cc_start: 0.8190 (m-80) cc_final: 0.7872 (m-80) REVERT: I 298 LYS cc_start: 0.8897 (tttt) cc_final: 0.8168 (tttm) REVERT: K 122 LEU cc_start: 0.8332 (mt) cc_final: 0.8036 (pp) REVERT: K 379 ASN cc_start: 0.7431 (p0) cc_final: 0.7114 (p0) REVERT: N 263 ASP cc_start: 0.7543 (t0) cc_final: 0.7121 (t0) outliers start: 52 outliers final: 34 residues processed: 325 average time/residue: 0.1337 time to fit residues: 66.8119 Evaluate side-chains 309 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain K residue 207 CYS Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain N residue 294 PHE Chi-restraints excluded: chain N residue 338 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 40 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 137 optimal weight: 0.3980 chunk 50 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123131 restraints weight = 33156.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125589 restraints weight = 22383.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126728 restraints weight = 16866.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127306 restraints weight = 14503.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127718 restraints weight = 13498.408| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19420 Z= 0.136 Angle : 0.716 37.166 26439 Z= 0.330 Chirality : 0.046 0.189 3028 Planarity : 0.004 0.048 3289 Dihedral : 8.665 89.555 3257 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.36 % Favored : 93.46 % Rotamer: Outliers : 2.29 % Allowed : 14.55 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.18), residues: 2310 helix: 0.42 (0.27), residues: 396 sheet: -0.67 (0.22), residues: 584 loop : -1.17 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 311 TYR 0.015 0.001 TYR I 278 PHE 0.019 0.002 PHE K 85 TRP 0.018 0.001 TRP E 35 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00310 (19345) covalent geometry : angle 0.69735 (26253) SS BOND : bond 0.00251 ( 39) SS BOND : angle 1.98177 ( 78) hydrogen bonds : bond 0.03545 ( 582) hydrogen bonds : angle 5.19600 ( 1635) link_ALPHA1-2 : bond 0.00307 ( 6) link_ALPHA1-2 : angle 1.80154 ( 18) link_ALPHA1-3 : bond 0.01116 ( 3) link_ALPHA1-3 : angle 1.34207 ( 9) link_ALPHA1-6 : bond 0.00563 ( 3) link_ALPHA1-6 : angle 1.41636 ( 9) link_BETA1-4 : bond 0.00638 ( 12) link_BETA1-4 : angle 2.12643 ( 36) link_NAG-ASN : bond 0.00444 ( 12) link_NAG-ASN : angle 2.39789 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 293 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8479 (mt) cc_final: 0.8231 (pp) REVERT: A 426 MET cc_start: 0.6857 (tmm) cc_final: 0.5782 (tmm) REVERT: A 467 THR cc_start: 0.6497 (m) cc_final: 0.6247 (p) REVERT: A 474 ASP cc_start: 0.5195 (OUTLIER) cc_final: 0.4867 (p0) REVERT: B 599 TRP cc_start: 0.8751 (m100) cc_final: 0.8297 (m100) REVERT: C 10 GLN cc_start: 0.7359 (mp10) cc_final: 0.6964 (mp-120) REVERT: C 111 TYR cc_start: 0.8502 (m-80) cc_final: 0.8291 (m-80) REVERT: E 47 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6818 (tm-30) REVERT: E 113 ASP cc_start: 0.8238 (t0) cc_final: 0.7992 (t0) REVERT: E 115 SER cc_start: 0.8823 (t) cc_final: 0.8601 (p) REVERT: H 10 GLN cc_start: 0.7045 (mp-120) cc_final: 0.6668 (mp-120) REVERT: H 81 MET cc_start: 0.8266 (tpp) cc_final: 0.7651 (ttp) REVERT: H 105 TYR cc_start: 0.8166 (m-80) cc_final: 0.7847 (m-80) REVERT: K 67 ASN cc_start: 0.7613 (t0) cc_final: 0.7129 (t0) REVERT: K 112 TRP cc_start: 0.7233 (t-100) cc_final: 0.6963 (t-100) REVERT: K 122 LEU cc_start: 0.8300 (mt) cc_final: 0.8016 (pp) REVERT: N 262 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.7009 (t-90) REVERT: N 263 ASP cc_start: 0.7612 (t0) cc_final: 0.7171 (t0) outliers start: 47 outliers final: 32 residues processed: 322 average time/residue: 0.1540 time to fit residues: 75.8969 Evaluate side-chains 307 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 273 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 262 HIS Chi-restraints excluded: chain N residue 294 PHE Chi-restraints excluded: chain N residue 338 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 23 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 216 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 22 optimal weight: 0.2980 chunk 150 optimal weight: 0.6980 chunk 208 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 315 GLN A 330 HIS B 519 ASN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS E 377 ASN H 3 GLN H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 270 GLN K 332 HIS M 39 GLN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 GLN N 292 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124015 restraints weight = 33089.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.126947 restraints weight = 22269.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128934 restraints weight = 16932.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.130287 restraints weight = 13970.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.131228 restraints weight = 12205.927| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19420 Z= 0.114 Angle : 0.673 32.121 26439 Z= 0.315 Chirality : 0.045 0.195 3028 Planarity : 0.004 0.050 3289 Dihedral : 7.857 89.747 3257 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.93 % Favored : 93.94 % Rotamer: Outliers : 2.64 % Allowed : 15.48 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.18), residues: 2310 helix: 0.60 (0.27), residues: 396 sheet: -0.46 (0.20), residues: 645 loop : -1.14 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 311 TYR 0.019 0.001 TYR I 319 PHE 0.018 0.001 PHE A 376 TRP 0.018 0.001 TRP E 35 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00254 (19345) covalent geometry : angle 0.65701 (26253) SS BOND : bond 0.00237 ( 39) SS BOND : angle 1.77814 ( 78) hydrogen bonds : bond 0.03207 ( 582) hydrogen bonds : angle 4.96892 ( 1635) link_ALPHA1-2 : bond 0.00309 ( 6) link_ALPHA1-2 : angle 1.70866 ( 18) link_ALPHA1-3 : bond 0.01056 ( 3) link_ALPHA1-3 : angle 1.36269 ( 9) link_ALPHA1-6 : bond 0.00820 ( 3) link_ALPHA1-6 : angle 1.32992 ( 9) link_BETA1-4 : bond 0.00598 ( 12) link_BETA1-4 : angle 1.88480 ( 36) link_NAG-ASN : bond 0.00453 ( 12) link_NAG-ASN : angle 2.18216 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 292 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 467 THR cc_start: 0.6432 (m) cc_final: 0.6229 (p) REVERT: A 474 ASP cc_start: 0.5172 (OUTLIER) cc_final: 0.4904 (p0) REVERT: C 10 GLN cc_start: 0.7334 (mp10) cc_final: 0.7075 (mp10) REVERT: C 38 ARG cc_start: 0.8940 (ttm-80) cc_final: 0.8382 (ttp-170) REVERT: E 113 ASP cc_start: 0.8165 (t0) cc_final: 0.7962 (t0) REVERT: E 115 SER cc_start: 0.8823 (t) cc_final: 0.8620 (p) REVERT: H 4 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5898 (mm) REVERT: H 10 GLN cc_start: 0.7039 (mp-120) cc_final: 0.6666 (mp-120) REVERT: H 81 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7678 (ttp) REVERT: H 105 TYR cc_start: 0.8162 (m-80) cc_final: 0.7829 (m-80) REVERT: I 301 ASN cc_start: 0.8399 (t0) cc_final: 0.8098 (t0) REVERT: K 67 ASN cc_start: 0.7599 (t0) cc_final: 0.7382 (t0) REVERT: K 428 MET cc_start: 0.4918 (tpp) cc_final: 0.4541 (tpp) REVERT: M 36 TRP cc_start: 0.8498 (m100) cc_final: 0.8119 (m100) REVERT: M 48 MET cc_start: 0.7527 (mtp) cc_final: 0.7253 (mtp) REVERT: M 90 ASP cc_start: 0.4770 (t70) cc_final: 0.4462 (t70) REVERT: N 262 HIS cc_start: 0.7096 (OUTLIER) cc_final: 0.6830 (t-90) REVERT: N 263 ASP cc_start: 0.7606 (t0) cc_final: 0.7168 (t0) outliers start: 54 outliers final: 37 residues processed: 327 average time/residue: 0.1575 time to fit residues: 78.2576 Evaluate side-chains 312 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 207 CYS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 262 HIS Chi-restraints excluded: chain N residue 294 PHE Chi-restraints excluded: chain N residue 338 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 188 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 222 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 525 GLN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113594 restraints weight = 33305.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116557 restraints weight = 22491.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118380 restraints weight = 16160.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119695 restraints weight = 13167.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.119914 restraints weight = 12042.513| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19420 Z= 0.131 Angle : 0.683 30.453 26439 Z= 0.322 Chirality : 0.045 0.216 3028 Planarity : 0.004 0.048 3289 Dihedral : 7.604 89.894 3257 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.45 % Favored : 93.42 % Rotamer: Outliers : 2.73 % Allowed : 16.36 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.18), residues: 2310 helix: 0.57 (0.27), residues: 397 sheet: -0.40 (0.22), residues: 569 loop : -1.13 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 293 TYR 0.016 0.001 TYR I 278 PHE 0.021 0.002 PHE K 85 TRP 0.017 0.001 TRP K 35 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00300 (19345) covalent geometry : angle 0.66648 (26253) SS BOND : bond 0.00170 ( 39) SS BOND : angle 1.82333 ( 78) hydrogen bonds : bond 0.03346 ( 582) hydrogen bonds : angle 4.91899 ( 1635) link_ALPHA1-2 : bond 0.00341 ( 6) link_ALPHA1-2 : angle 1.72553 ( 18) link_ALPHA1-3 : bond 0.01053 ( 3) link_ALPHA1-3 : angle 1.38447 ( 9) link_ALPHA1-6 : bond 0.00900 ( 3) link_ALPHA1-6 : angle 1.21254 ( 9) link_BETA1-4 : bond 0.00610 ( 12) link_BETA1-4 : angle 1.83972 ( 36) link_NAG-ASN : bond 0.00447 ( 12) link_NAG-ASN : angle 2.35168 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 288 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 THR cc_start: 0.6331 (m) cc_final: 0.6063 (p) REVERT: A 474 ASP cc_start: 0.5361 (OUTLIER) cc_final: 0.5102 (p0) REVERT: B 599 TRP cc_start: 0.8678 (m100) cc_final: 0.8227 (m100) REVERT: C 10 GLN cc_start: 0.7344 (mp10) cc_final: 0.7001 (mp10) REVERT: C 70 MET cc_start: 0.8408 (mtt) cc_final: 0.8128 (mtp) REVERT: E 113 ASP cc_start: 0.8214 (t0) cc_final: 0.7995 (t0) REVERT: E 115 SER cc_start: 0.8827 (t) cc_final: 0.8568 (p) REVERT: H 4 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5945 (mm) REVERT: H 10 GLN cc_start: 0.6877 (mp-120) cc_final: 0.6521 (mp-120) REVERT: H 105 TYR cc_start: 0.8250 (m-80) cc_final: 0.7921 (m-80) REVERT: I 301 ASN cc_start: 0.8446 (t0) cc_final: 0.8165 (t0) REVERT: K 67 ASN cc_start: 0.7908 (t0) cc_final: 0.7565 (t0) REVERT: K 379 ASN cc_start: 0.7327 (OUTLIER) cc_final: 0.6882 (p0) REVERT: K 428 MET cc_start: 0.4934 (tpp) cc_final: 0.4468 (tpp) REVERT: N 262 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6001 (t-90) REVERT: N 263 ASP cc_start: 0.7745 (t0) cc_final: 0.7470 (t0) REVERT: N 278 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7089 (t80) outliers start: 56 outliers final: 40 residues processed: 319 average time/residue: 0.1544 time to fit residues: 75.2450 Evaluate side-chains 318 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 207 CYS Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 379 ASN Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 262 HIS Chi-restraints excluded: chain N residue 278 TYR Chi-restraints excluded: chain N residue 294 PHE Chi-restraints excluded: chain N residue 328 THR Chi-restraints excluded: chain N residue 338 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 29 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS C 3 GLN C 54 GLN ** D 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN H 3 GLN H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN K 332 HIS ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110475 restraints weight = 33894.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.113102 restraints weight = 24229.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114954 restraints weight = 17456.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.115864 restraints weight = 14049.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.116196 restraints weight = 13149.400| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19420 Z= 0.190 Angle : 0.738 30.038 26439 Z= 0.353 Chirality : 0.047 0.238 3028 Planarity : 0.004 0.052 3289 Dihedral : 7.770 89.814 3257 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.45 % Favored : 92.42 % Rotamer: Outliers : 2.73 % Allowed : 17.19 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.18), residues: 2310 helix: 0.36 (0.27), residues: 396 sheet: -0.47 (0.21), residues: 589 loop : -1.31 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 311 TYR 0.022 0.002 TYR I 278 PHE 0.014 0.002 PHE H 64 TRP 0.023 0.002 TRP E 35 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00444 (19345) covalent geometry : angle 0.72070 (26253) SS BOND : bond 0.00229 ( 39) SS BOND : angle 1.94922 ( 78) hydrogen bonds : bond 0.03736 ( 582) hydrogen bonds : angle 5.12892 ( 1635) link_ALPHA1-2 : bond 0.00370 ( 6) link_ALPHA1-2 : angle 1.81092 ( 18) link_ALPHA1-3 : bond 0.01010 ( 3) link_ALPHA1-3 : angle 1.45424 ( 9) link_ALPHA1-6 : bond 0.00970 ( 3) link_ALPHA1-6 : angle 0.97703 ( 9) link_BETA1-4 : bond 0.00665 ( 12) link_BETA1-4 : angle 2.03877 ( 36) link_NAG-ASN : bond 0.00488 ( 12) link_NAG-ASN : angle 2.59573 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 285 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 474 ASP cc_start: 0.5329 (OUTLIER) cc_final: 0.5081 (p0) REVERT: C 10 GLN cc_start: 0.7355 (mp10) cc_final: 0.6694 (mp10) REVERT: E 494 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8632 (tt) REVERT: F 590 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8397 (tp40) REVERT: H 4 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5916 (mm) REVERT: H 10 GLN cc_start: 0.6840 (mp-120) cc_final: 0.6483 (mp-120) REVERT: H 65 GLN cc_start: 0.8149 (tp40) cc_final: 0.7738 (tp40) REVERT: H 105 TYR cc_start: 0.8308 (m-80) cc_final: 0.8021 (m-80) REVERT: K 67 ASN cc_start: 0.8336 (t0) cc_final: 0.7816 (t0) REVERT: K 270 LYS cc_start: 0.7735 (mptt) cc_final: 0.6994 (tmtt) REVERT: K 379 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7236 (p0) REVERT: N 262 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.6035 (t-90) REVERT: N 278 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7185 (t80) REVERT: N 319 TYR cc_start: 0.8308 (m-80) cc_final: 0.8106 (m-80) outliers start: 56 outliers final: 41 residues processed: 316 average time/residue: 0.1506 time to fit residues: 73.2396 Evaluate side-chains 314 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 267 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain K residue 207 CYS Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 379 ASN Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 262 HIS Chi-restraints excluded: chain N residue 278 TYR Chi-restraints excluded: chain N residue 328 THR Chi-restraints excluded: chain N residue 338 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 1 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 225 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS ** D 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 HIS M 39 GLN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112324 restraints weight = 33598.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115171 restraints weight = 23097.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117185 restraints weight = 16802.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118043 restraints weight = 13342.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118322 restraints weight = 12460.355| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19420 Z= 0.143 Angle : 0.717 28.989 26439 Z= 0.342 Chirality : 0.046 0.211 3028 Planarity : 0.004 0.050 3289 Dihedral : 7.325 89.684 3257 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.54 % Favored : 93.33 % Rotamer: Outliers : 2.29 % Allowed : 18.02 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.18), residues: 2310 helix: 0.51 (0.27), residues: 397 sheet: -0.39 (0.22), residues: 571 loop : -1.23 (0.18), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 311 TYR 0.020 0.001 TYR E 361 PHE 0.022 0.002 PHE K 85 TRP 0.024 0.001 TRP E 35 HIS 0.013 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00330 (19345) covalent geometry : angle 0.70125 (26253) SS BOND : bond 0.00199 ( 39) SS BOND : angle 1.80254 ( 78) hydrogen bonds : bond 0.03490 ( 582) hydrogen bonds : angle 5.04798 ( 1635) link_ALPHA1-2 : bond 0.00352 ( 6) link_ALPHA1-2 : angle 1.70870 ( 18) link_ALPHA1-3 : bond 0.01083 ( 3) link_ALPHA1-3 : angle 1.37725 ( 9) link_ALPHA1-6 : bond 0.01026 ( 3) link_ALPHA1-6 : angle 0.93780 ( 9) link_BETA1-4 : bond 0.00617 ( 12) link_BETA1-4 : angle 1.87466 ( 36) link_NAG-ASN : bond 0.00471 ( 12) link_NAG-ASN : angle 2.43939 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LYS cc_start: 0.7263 (mmtm) cc_final: 0.6585 (tmtt) REVERT: A 293 GLU cc_start: 0.7810 (tt0) cc_final: 0.7589 (tp30) REVERT: A 467 THR cc_start: 0.6417 (m) cc_final: 0.6133 (p) REVERT: A 474 ASP cc_start: 0.5325 (OUTLIER) cc_final: 0.5115 (p0) REVERT: B 599 TRP cc_start: 0.8694 (m100) cc_final: 0.8249 (m100) REVERT: C 65 GLN cc_start: 0.8283 (tp40) cc_final: 0.8059 (tp40) REVERT: E 494 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8579 (tt) REVERT: F 590 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8419 (tp40) REVERT: H 3 GLN cc_start: 0.6500 (mp10) cc_final: 0.6170 (mp10) REVERT: H 4 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5925 (mm) REVERT: H 10 GLN cc_start: 0.6902 (mp-120) cc_final: 0.6551 (mp-120) REVERT: H 105 TYR cc_start: 0.8252 (m-80) cc_final: 0.7958 (m-80) REVERT: I 301 ASN cc_start: 0.8294 (t0) cc_final: 0.8008 (t0) REVERT: K 67 ASN cc_start: 0.8342 (t0) cc_final: 0.7824 (t0) REVERT: N 262 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6014 (t-90) REVERT: N 278 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7187 (t80) outliers start: 47 outliers final: 36 residues processed: 311 average time/residue: 0.1563 time to fit residues: 74.0335 Evaluate side-chains 313 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 272 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 207 CYS Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 262 HIS Chi-restraints excluded: chain N residue 278 TYR Chi-restraints excluded: chain N residue 294 PHE Chi-restraints excluded: chain N residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 138 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 171 optimal weight: 0.4980 chunk 224 optimal weight: 0.0470 chunk 61 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 overall best weight: 3.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 583 ASN C 10 GLN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.134142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.111076 restraints weight = 33613.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113914 restraints weight = 23534.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116076 restraints weight = 16830.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116643 restraints weight = 13159.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117153 restraints weight = 12435.730| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19420 Z= 0.175 Angle : 0.756 37.477 26439 Z= 0.357 Chirality : 0.047 0.207 3028 Planarity : 0.004 0.050 3289 Dihedral : 7.287 89.611 3257 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.66 % Favored : 92.21 % Rotamer: Outliers : 2.15 % Allowed : 18.16 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.18), residues: 2310 helix: 0.42 (0.27), residues: 397 sheet: -0.42 (0.22), residues: 571 loop : -1.29 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 311 TYR 0.020 0.002 TYR I 278 PHE 0.013 0.002 PHE A 376 TRP 0.032 0.002 TRP K 35 HIS 0.014 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00410 (19345) covalent geometry : angle 0.74050 (26253) SS BOND : bond 0.00293 ( 39) SS BOND : angle 1.92290 ( 78) hydrogen bonds : bond 0.03568 ( 582) hydrogen bonds : angle 5.11280 ( 1635) link_ALPHA1-2 : bond 0.00319 ( 6) link_ALPHA1-2 : angle 1.74101 ( 18) link_ALPHA1-3 : bond 0.00954 ( 3) link_ALPHA1-3 : angle 1.43935 ( 9) link_ALPHA1-6 : bond 0.01122 ( 3) link_ALPHA1-6 : angle 0.84753 ( 9) link_BETA1-4 : bond 0.00629 ( 12) link_BETA1-4 : angle 1.86346 ( 36) link_NAG-ASN : bond 0.00474 ( 12) link_NAG-ASN : angle 2.51285 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7784 (tt0) cc_final: 0.7511 (tp30) REVERT: A 474 ASP cc_start: 0.5432 (OUTLIER) cc_final: 0.5199 (p0) REVERT: E 494 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8580 (tt) REVERT: F 590 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8422 (tp40) REVERT: H 4 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.5976 (mm) REVERT: H 10 GLN cc_start: 0.6827 (mp-120) cc_final: 0.6474 (mp-120) REVERT: H 65 GLN cc_start: 0.8133 (tp40) cc_final: 0.7741 (tp40) REVERT: H 105 TYR cc_start: 0.8310 (m-80) cc_final: 0.8027 (m-80) REVERT: K 67 ASN cc_start: 0.8446 (t0) cc_final: 0.7945 (t0) REVERT: K 379 ASN cc_start: 0.7646 (p0) cc_final: 0.7274 (p0) REVERT: M 111 TYR cc_start: 0.8556 (m-10) cc_final: 0.8299 (m-80) REVERT: N 262 HIS cc_start: 0.7161 (OUTLIER) cc_final: 0.5985 (t-90) REVERT: N 263 ASP cc_start: 0.7835 (t0) cc_final: 0.7601 (t0) REVERT: N 278 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7285 (t80) outliers start: 44 outliers final: 35 residues processed: 305 average time/residue: 0.1558 time to fit residues: 72.6092 Evaluate side-chains 315 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 207 CYS Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 262 HIS Chi-restraints excluded: chain N residue 278 TYR Chi-restraints excluded: chain N residue 294 PHE Chi-restraints excluded: chain N residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 36 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 GLN E 377 ASN H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 632 GLN ** N 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114121 restraints weight = 33629.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117031 restraints weight = 22747.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119115 restraints weight = 16674.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119838 restraints weight = 13233.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120087 restraints weight = 12310.438| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19420 Z= 0.126 Angle : 0.722 35.260 26439 Z= 0.341 Chirality : 0.045 0.208 3028 Planarity : 0.004 0.048 3289 Dihedral : 6.864 89.708 3257 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.28 % Favored : 93.59 % Rotamer: Outliers : 2.25 % Allowed : 18.46 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.18), residues: 2310 helix: 0.61 (0.28), residues: 396 sheet: -0.24 (0.21), residues: 595 loop : -1.27 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 311 TYR 0.014 0.001 TYR I 278 PHE 0.020 0.001 PHE K 85 TRP 0.035 0.001 TRP K 35 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00289 (19345) covalent geometry : angle 0.70830 (26253) SS BOND : bond 0.00237 ( 39) SS BOND : angle 1.78018 ( 78) hydrogen bonds : bond 0.03294 ( 582) hydrogen bonds : angle 4.98994 ( 1635) link_ALPHA1-2 : bond 0.00331 ( 6) link_ALPHA1-2 : angle 1.65051 ( 18) link_ALPHA1-3 : bond 0.01072 ( 3) link_ALPHA1-3 : angle 1.28760 ( 9) link_ALPHA1-6 : bond 0.01121 ( 3) link_ALPHA1-6 : angle 0.92948 ( 9) link_BETA1-4 : bond 0.00593 ( 12) link_BETA1-4 : angle 1.74200 ( 36) link_NAG-ASN : bond 0.00455 ( 12) link_NAG-ASN : angle 2.32320 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2946.42 seconds wall clock time: 52 minutes 12.30 seconds (3132.30 seconds total)