Starting phenix.real_space_refine on Mon Jun 16 13:10:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8saq_40275/06_2025/8saq_40275_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8saq_40275/06_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_40275/06_2025/8saq_40275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8saq_40275/06_2025/8saq_40275.map" model { file = "/net/cci-nas-00/data/ceres_data/8saq_40275/06_2025/8saq_40275_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8saq_40275/06_2025/8saq_40275_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.44, per 1000 atoms: 0.55 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: 4.63 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.31 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: 5.89 Time building geometry restraints manager: 5.50 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 522 or resid 601 throu \ gh 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: 0.370 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 40.620 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (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 TRP 0.025 0.002 TRP A 35 HIS 0.030 0.003 HIS A 287 PHE 0.032 0.002 PHE H 114 TYR 0.034 0.002 TYR D 546 ARG 0.016 0.001 ARG M 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 12) link_NAG-ASN : angle 2.12972 ( 36) 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_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) hydrogen bonds : bond 0.22498 ( 582) hydrogen bonds : angle 8.59229 ( 1635) SS BOND : bond 0.00553 ( 39) SS BOND : angle 2.27370 ( 78) covalent geometry : bond 0.00545 (19345) covalent geometry : angle 0.88454 (26253) *********************** 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 : 2.091 Fit side-chains 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: 0.5766 (tmm) REVERT: B 519 ASN cc_start: 0.8801 (t0) cc_final: 0.8429 (t0) REVERT: B 577 LYS cc_start: 0.7481 (mmmt) cc_final: 0.7077 (tptp) REVERT: D 537 ILE cc_start: 0.6582 (mm) cc_final: 0.6373 (mm) REVERT: E 47 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6874 (tm-30) REVERT: E 280 ASN cc_start: 0.7945 (m-40) cc_final: 0.7350 (t0) REVERT: F 635 ILE cc_start: 0.8616 (mm) cc_final: 0.8311 (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: 0.8058 (ttp80) REVERT: H 75 SER cc_start: 0.7843 (p) cc_final: 0.7293 (p) REVERT: I 298 LYS cc_start: 0.8785 (tttt) cc_final: 0.8156 (tttp) REVERT: K 219 TYR cc_start: 0.7947 (m-10) cc_final: 0.7708 (m-80) REVERT: K 428 MET cc_start: 0.5168 (tpp) cc_final: 0.4626 (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: 0.3207 time to fit residues: 189.4848 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 : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 8.9990 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 207 optimal weight: 0.0870 overall best weight: 1.7562 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.146296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124196 restraints weight = 33082.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126658 restraints weight = 22910.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128352 restraints weight = 17077.998| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19420 Z= 0.144 Angle : 0.749 32.980 26439 Z= 0.364 Chirality : 0.048 0.263 3028 Planarity : 0.004 0.050 3289 Dihedral : 11.146 88.560 3257 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.71 % Favored : 94.07 % Rotamer: Outliers : 1.32 % Allowed : 7.76 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.18), residues: 2310 helix: 0.04 (0.27), residues: 392 sheet: -0.80 (0.20), residues: 687 loop : -1.26 (0.19), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 35 HIS 0.006 0.001 HIS A 287 PHE 0.023 0.002 PHE K 85 TYR 0.023 0.002 TYR E 217 ARG 0.005 0.001 ARG N 293 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 12) link_NAG-ASN : angle 2.32923 ( 36) link_ALPHA1-6 : bond 0.00316 ( 3) link_ALPHA1-6 : angle 1.46764 ( 9) link_BETA1-4 : bond 0.00710 ( 12) link_BETA1-4 : angle 2.52567 ( 36) link_ALPHA1-2 : bond 0.00459 ( 6) link_ALPHA1-2 : angle 2.22038 ( 18) link_ALPHA1-3 : bond 0.01643 ( 3) link_ALPHA1-3 : angle 1.01104 ( 9) hydrogen bonds : bond 0.04412 ( 582) hydrogen bonds : angle 5.96259 ( 1635) SS BOND : bond 0.00729 ( 39) SS BOND : angle 2.59407 ( 78) covalent geometry : bond 0.00317 (19345) covalent geometry : angle 0.72417 (26253) *********************** 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 335 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 308 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.7948 (m-40) cc_final: 0.7670 (m-40) REVERT: A 426 MET cc_start: 0.6939 (tmm) cc_final: 0.6008 (tmm) REVERT: B 506 MET cc_start: 0.7621 (mtp) cc_final: 0.7366 (mtp) REVERT: B 519 ASN cc_start: 0.9084 (t0) cc_final: 0.8818 (t0) REVERT: D 625 TYR cc_start: 0.7655 (m-80) cc_final: 0.7302 (m-80) REVERT: E 113 ASP cc_start: 0.8162 (t0) cc_final: 0.7915 (t0) REVERT: E 115 SER cc_start: 0.8811 (t) cc_final: 0.8564 (p) REVERT: E 377 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.7098 (p0) REVERT: F 626 MET cc_start: 0.6909 (ttm) cc_final: 0.6424 (ttm) REVERT: F 634 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7298 (mt-10) REVERT: H 3 GLN cc_start: 0.7181 (tp-100) cc_final: 0.6956 (mp10) REVERT: H 4 LEU cc_start: 0.6402 (mm) cc_final: 0.6161 (mm) REVERT: H 10 GLN cc_start: 0.7044 (mp-120) cc_final: 0.6681 (mp-120) REVERT: I 298 LYS cc_start: 0.8955 (tttt) cc_final: 0.8301 (tttp) REVERT: M 48 MET cc_start: 0.7491 (mtp) cc_final: 0.7078 (mtp) REVERT: N 270 GLN cc_start: 0.5654 (pt0) cc_final: 0.5347 (pt0) outliers start: 27 outliers final: 15 residues processed: 319 average time/residue: 0.2981 time to fit residues: 146.0348 Evaluate side-chains 292 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 276 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 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 89 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 607 ASN E 66 HIS E 114 GLN H 6 GLN H 54 GLN K 480 ASN M 6 GLN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118773 restraints weight = 33258.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121202 restraints weight = 22935.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122162 restraints weight = 17636.631| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19420 Z= 0.272 Angle : 0.837 35.590 26439 Z= 0.403 Chirality : 0.050 0.244 3028 Planarity : 0.005 0.054 3289 Dihedral : 10.702 89.145 3257 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.84 % Favored : 91.99 % Rotamer: Outliers : 2.10 % Allowed : 11.33 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 2310 helix: -0.12 (0.27), residues: 389 sheet: -0.95 (0.21), residues: 618 loop : -1.36 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 35 HIS 0.012 0.003 HIS M 35 PHE 0.019 0.003 PHE A 468 TYR 0.033 0.002 TYR I 278 ARG 0.007 0.001 ARG I 293 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 12) link_NAG-ASN : angle 2.81862 ( 36) link_ALPHA1-6 : bond 0.00251 ( 3) link_ALPHA1-6 : angle 1.42375 ( 9) link_BETA1-4 : bond 0.00804 ( 12) link_BETA1-4 : angle 2.49568 ( 36) link_ALPHA1-2 : bond 0.00362 ( 6) link_ALPHA1-2 : angle 2.11364 ( 18) link_ALPHA1-3 : bond 0.01017 ( 3) link_ALPHA1-3 : angle 1.53319 ( 9) hydrogen bonds : bond 0.04749 ( 582) hydrogen bonds : angle 5.86809 ( 1635) SS BOND : bond 0.00642 ( 39) SS BOND : angle 2.48715 ( 78) covalent geometry : bond 0.00641 (19345) covalent geometry : angle 0.81398 (26253) *********************** 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 343 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 300 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8424 (mt) cc_final: 0.8054 (pp) REVERT: A 426 MET cc_start: 0.7041 (tmm) cc_final: 0.6064 (tmm) REVERT: C 10 GLN cc_start: 0.7409 (mp10) cc_final: 0.6996 (mp10) REVERT: C 48 MET cc_start: 0.7666 (mtp) cc_final: 0.7381 (mtp) REVERT: E 113 ASP cc_start: 0.8316 (t0) cc_final: 0.8054 (t0) REVERT: F 626 MET cc_start: 0.6801 (ttm) cc_final: 0.6056 (ttm) REVERT: F 634 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7541 (mt-10) REVERT: H 10 GLN cc_start: 0.7222 (mp-120) cc_final: 0.6708 (mp-120) REVERT: H 105 TYR cc_start: 0.8270 (m-80) cc_final: 0.7993 (m-80) REVERT: I 298 LYS cc_start: 0.8954 (tttt) cc_final: 0.8340 (tttp) REVERT: K 379 ASN cc_start: 0.7551 (p0) cc_final: 0.7333 (p0) REVERT: L 532 MET cc_start: 0.8041 (mtp) cc_final: 0.7682 (mtp) REVERT: N 263 ASP cc_start: 0.7700 (t0) cc_final: 0.7290 (t0) REVERT: N 270 GLN cc_start: 0.5868 (pt0) cc_final: 0.5521 (pt0) outliers start: 43 outliers final: 30 residues processed: 325 average time/residue: 0.3170 time to fit residues: 160.1488 Evaluate side-chains 301 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 2.628 ------------------------------------------------------------------------------- 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 180 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 C residue 6 GLN 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 109 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 345 VAL 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 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 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 N residue 259 VAL 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 86 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 156 optimal weight: 40.0000 chunk 165 optimal weight: 0.2980 chunk 129 optimal weight: 10.0000 chunk 208 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 330 HIS C 3 GLN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.146338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124157 restraints weight = 33030.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126673 restraints weight = 23667.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128658 restraints weight = 17525.459| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19420 Z= 0.118 Angle : 0.707 36.397 26439 Z= 0.332 Chirality : 0.045 0.185 3028 Planarity : 0.004 0.049 3289 Dihedral : 9.031 89.314 3257 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.32 % Favored : 94.50 % Rotamer: Outliers : 1.90 % Allowed : 13.09 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 2310 helix: 0.24 (0.26), residues: 397 sheet: -0.65 (0.20), residues: 659 loop : -1.22 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 35 HIS 0.007 0.001 HIS A 374 PHE 0.028 0.002 PHE A 376 TYR 0.013 0.001 TYR K 488 ARG 0.004 0.000 ARG I 293 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 12) link_NAG-ASN : angle 2.31863 ( 36) link_ALPHA1-6 : bond 0.00467 ( 3) link_ALPHA1-6 : angle 1.52946 ( 9) link_BETA1-4 : bond 0.00615 ( 12) link_BETA1-4 : angle 2.19545 ( 36) link_ALPHA1-2 : bond 0.00253 ( 6) link_ALPHA1-2 : angle 1.83535 ( 18) link_ALPHA1-3 : bond 0.01253 ( 3) link_ALPHA1-3 : angle 1.32978 ( 9) hydrogen bonds : bond 0.03518 ( 582) hydrogen bonds : angle 5.29691 ( 1635) SS BOND : bond 0.00304 ( 39) SS BOND : angle 1.86233 ( 78) covalent geometry : bond 0.00257 (19345) covalent geometry : angle 0.68954 (26253) *********************** 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 338 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 299 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8398 (mt) cc_final: 0.8112 (pp) REVERT: A 426 MET cc_start: 0.6916 (tmm) cc_final: 0.5841 (tmm) REVERT: A 467 THR cc_start: 0.6446 (m) cc_final: 0.6186 (p) REVERT: A 474 ASP cc_start: 0.5525 (OUTLIER) cc_final: 0.5061 (p0) REVERT: B 506 MET cc_start: 0.7619 (mtp) cc_final: 0.7416 (mtp) REVERT: B 599 TRP cc_start: 0.8731 (m100) cc_final: 0.8268 (m100) REVERT: C 10 GLN cc_start: 0.7355 (mp10) cc_final: 0.7034 (mp10) REVERT: C 48 MET cc_start: 0.7645 (mtp) cc_final: 0.7254 (mtp) REVERT: C 70 MET cc_start: 0.8327 (mtm) cc_final: 0.8098 (mtm) REVERT: C 90 ASP cc_start: 0.5425 (t70) cc_final: 0.5193 (t0) REVERT: E 113 ASP cc_start: 0.8206 (t0) cc_final: 0.7940 (t0) REVERT: E 115 SER cc_start: 0.8815 (t) cc_final: 0.8603 (p) REVERT: E 211 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7053 (tm-30) REVERT: E 377 ASN cc_start: 0.7288 (OUTLIER) cc_final: 0.7055 (p0) REVERT: F 626 MET cc_start: 0.6749 (ttm) cc_final: 0.6034 (ttm) REVERT: H 3 GLN cc_start: 0.7049 (tp-100) cc_final: 0.6781 (mp10) REVERT: H 10 GLN cc_start: 0.7017 (mp-120) cc_final: 0.6670 (mp-120) REVERT: K 122 LEU cc_start: 0.8323 (mt) cc_final: 0.7972 (pp) REVERT: N 263 ASP cc_start: 0.7525 (t0) cc_final: 0.7112 (t0) REVERT: N 270 GLN cc_start: 0.5956 (pt0) cc_final: 0.5612 (pt0) REVERT: N 301 ASN cc_start: 0.8391 (t0) cc_final: 0.7995 (t0) outliers start: 39 outliers final: 24 residues processed: 325 average time/residue: 0.3788 time to fit residues: 192.6813 Evaluate side-chains 305 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 279 time to evaluate : 2.436 ------------------------------------------------------------------------------- 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 247 CYS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain C residue 6 GLN 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 109 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 481 SER 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 H residue 122 LEU Chi-restraints excluded: chain I residue 338 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 218 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 168 optimal weight: 0.0070 chunk 64 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 overall best weight: 6.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS A 330 HIS B 519 ASN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 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 = 0.3783 r_free = 0.3783 target = 0.138022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115961 restraints weight = 33973.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.117826 restraints weight = 24135.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119268 restraints weight = 19155.469| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 19420 Z= 0.321 Angle : 0.859 38.455 26439 Z= 0.410 Chirality : 0.050 0.194 3028 Planarity : 0.005 0.056 3289 Dihedral : 9.909 89.334 3257 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.74 % Favored : 91.13 % Rotamer: Outliers : 3.32 % Allowed : 15.38 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2310 helix: -0.15 (0.26), residues: 390 sheet: -0.93 (0.21), residues: 612 loop : -1.48 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 427 HIS 0.018 0.003 HIS A 374 PHE 0.023 0.003 PHE C 32 TYR 0.031 0.002 TYR I 278 ARG 0.005 0.001 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00680 ( 12) link_NAG-ASN : angle 2.89245 ( 36) link_ALPHA1-6 : bond 0.00393 ( 3) link_ALPHA1-6 : angle 1.29735 ( 9) link_BETA1-4 : bond 0.00773 ( 12) link_BETA1-4 : angle 2.41602 ( 36) link_ALPHA1-2 : bond 0.00425 ( 6) link_ALPHA1-2 : angle 2.05111 ( 18) link_ALPHA1-3 : bond 0.00802 ( 3) link_ALPHA1-3 : angle 1.53706 ( 9) hydrogen bonds : bond 0.04639 ( 582) hydrogen bonds : angle 5.73078 ( 1635) SS BOND : bond 0.00570 ( 39) SS BOND : angle 2.42037 ( 78) covalent geometry : bond 0.00757 (19345) covalent geometry : angle 0.83807 (26253) *********************** 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 359 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 291 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8450 (mt) cc_final: 0.8099 (pp) REVERT: A 426 MET cc_start: 0.7063 (tmm) cc_final: 0.5927 (tmm) REVERT: A 474 ASP cc_start: 0.5683 (OUTLIER) cc_final: 0.5381 (p0) REVERT: C 10 GLN cc_start: 0.7412 (mp10) cc_final: 0.6893 (mp10) REVERT: C 48 MET cc_start: 0.7679 (mtp) cc_final: 0.7435 (mtp) REVERT: D 642 LYS cc_start: 0.6497 (tttm) cc_final: 0.6164 (tptt) REVERT: E 113 ASP cc_start: 0.8349 (t0) cc_final: 0.8073 (t0) REVERT: E 377 ASN cc_start: 0.7640 (p0) cc_final: 0.7399 (p0) REVERT: F 634 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7260 (mt-10) REVERT: H 3 GLN cc_start: 0.7144 (tp-100) cc_final: 0.6448 (mp10) REVERT: H 10 GLN cc_start: 0.7039 (mp-120) cc_final: 0.6581 (mp-120) REVERT: H 81 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.8020 (ttt) REVERT: I 298 LYS cc_start: 0.8930 (tttt) cc_final: 0.8396 (tttp) REVERT: K 213 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7355 (tm-30) REVERT: K 379 ASN cc_start: 0.7760 (p0) cc_final: 0.7536 (p0) REVERT: M 48 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8267 (mtp) REVERT: M 90 ASP cc_start: 0.5287 (t70) cc_final: 0.5069 (t0) REVERT: N 262 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.6220 (t-90) REVERT: N 263 ASP cc_start: 0.7684 (t0) cc_final: 0.7463 (t0) REVERT: N 270 GLN cc_start: 0.5902 (pt0) cc_final: 0.5626 (pt0) outliers start: 68 outliers final: 45 residues processed: 329 average time/residue: 0.3023 time to fit residues: 155.2579 Evaluate side-chains 323 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 245 VAL 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 605 LEU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain D residue 538 THR 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 95 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 249 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 109 ILE 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 292 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 343 THR 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 631 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain N residue 262 HIS Chi-restraints excluded: chain N residue 318 TYR Chi-restraints excluded: chain N residue 328 THR 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 75 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118929 restraints weight = 33863.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121597 restraints weight = 23061.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122275 restraints weight = 17301.718| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19420 Z= 0.195 Angle : 0.756 34.834 26439 Z= 0.359 Chirality : 0.047 0.184 3028 Planarity : 0.004 0.056 3289 Dihedral : 9.223 89.169 3257 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.67 % Favored : 93.20 % Rotamer: Outliers : 3.03 % Allowed : 17.33 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2310 helix: -0.02 (0.26), residues: 395 sheet: -0.87 (0.21), residues: 606 loop : -1.43 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 35 HIS 0.013 0.002 HIS A 374 PHE 0.024 0.002 PHE K 85 TYR 0.020 0.002 TYR I 278 ARG 0.005 0.000 ARG N 311 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 12) link_NAG-ASN : angle 2.65344 ( 36) link_ALPHA1-6 : bond 0.00419 ( 3) link_ALPHA1-6 : angle 1.47660 ( 9) link_BETA1-4 : bond 0.00678 ( 12) link_BETA1-4 : angle 2.22812 ( 36) link_ALPHA1-2 : bond 0.00316 ( 6) link_ALPHA1-2 : angle 1.78457 ( 18) link_ALPHA1-3 : bond 0.01019 ( 3) link_ALPHA1-3 : angle 1.38890 ( 9) hydrogen bonds : bond 0.03937 ( 582) hydrogen bonds : angle 5.44031 ( 1635) SS BOND : bond 0.00265 ( 39) SS BOND : angle 2.08488 ( 78) covalent geometry : bond 0.00456 (19345) covalent geometry : angle 0.73657 (26253) *********************** 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 352 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 290 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8347 (mt) cc_final: 0.8105 (pp) REVERT: A 426 MET cc_start: 0.6960 (tmm) cc_final: 0.5792 (tmm) REVERT: A 474 ASP cc_start: 0.5795 (OUTLIER) cc_final: 0.5435 (p0) REVERT: B 599 TRP cc_start: 0.8790 (m100) cc_final: 0.8390 (m100) REVERT: C 10 GLN cc_start: 0.7442 (mp10) cc_final: 0.6939 (mp10) REVERT: C 48 MET cc_start: 0.7589 (mtp) cc_final: 0.7320 (mtp) REVERT: C 65 GLN cc_start: 0.8381 (tp40) cc_final: 0.8019 (tp40) REVERT: D 625 TYR cc_start: 0.7931 (m-80) cc_final: 0.7665 (m-80) REVERT: E 113 ASP cc_start: 0.8317 (t0) cc_final: 0.8075 (t0) REVERT: E 115 SER cc_start: 0.8869 (t) cc_final: 0.8617 (p) REVERT: E 377 ASN cc_start: 0.7765 (p0) cc_final: 0.7492 (p0) REVERT: F 634 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7268 (mt-10) REVERT: H 3 GLN cc_start: 0.7047 (tp-100) cc_final: 0.6563 (mp10) REVERT: H 10 GLN cc_start: 0.7099 (mp-120) cc_final: 0.6678 (mp-120) REVERT: H 81 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7770 (ttp) REVERT: I 270 GLN cc_start: 0.6319 (pt0) cc_final: 0.6116 (pt0) REVERT: I 298 LYS cc_start: 0.8915 (tttt) cc_final: 0.8132 (tttp) REVERT: K 67 ASN cc_start: 0.7914 (t0) cc_final: 0.7566 (t0) REVERT: K 122 LEU cc_start: 0.8388 (mt) cc_final: 0.8094 (pp) REVERT: K 213 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7366 (tm-30) REVERT: K 379 ASN cc_start: 0.7603 (p0) cc_final: 0.7279 (p0) REVERT: M 46 GLN cc_start: 0.7537 (mt0) cc_final: 0.7333 (mt0) REVERT: M 90 ASP cc_start: 0.5193 (t70) cc_final: 0.4911 (t70) REVERT: N 262 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.6191 (t-90) REVERT: N 270 GLN cc_start: 0.6043 (pt0) cc_final: 0.5802 (pt0) REVERT: N 278 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.6874 (t80) outliers start: 62 outliers final: 46 residues processed: 330 average time/residue: 0.2912 time to fit residues: 148.4296 Evaluate side-chains 325 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER 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 444 THR Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 548 VAL 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 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 180 ASP Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain F residue 569 THR 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 I residue 275 VAL 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 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 L residue 568 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 249 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 23 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 219 optimal weight: 0.2980 chunk 155 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118853 restraints weight = 33613.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121538 restraints weight = 23088.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122353 restraints weight = 17334.582| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2777 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= 0.179 Angle : 0.737 32.464 26439 Z= 0.351 Chirality : 0.046 0.192 3028 Planarity : 0.004 0.058 3289 Dihedral : 8.847 89.115 3257 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.66 % Favored : 92.21 % Rotamer: Outliers : 3.56 % Allowed : 17.24 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.17), residues: 2310 helix: 0.05 (0.27), residues: 394 sheet: -0.85 (0.20), residues: 614 loop : -1.44 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 35 HIS 0.009 0.002 HIS A 374 PHE 0.019 0.002 PHE E 85 TYR 0.020 0.002 TYR I 278 ARG 0.006 0.000 ARG N 311 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 12) link_NAG-ASN : angle 2.58474 ( 36) link_ALPHA1-6 : bond 0.00519 ( 3) link_ALPHA1-6 : angle 1.38638 ( 9) link_BETA1-4 : bond 0.00646 ( 12) link_BETA1-4 : angle 2.11255 ( 36) link_ALPHA1-2 : bond 0.00326 ( 6) link_ALPHA1-2 : angle 1.73289 ( 18) link_ALPHA1-3 : bond 0.01037 ( 3) link_ALPHA1-3 : angle 1.45100 ( 9) hydrogen bonds : bond 0.03804 ( 582) hydrogen bonds : angle 5.34259 ( 1635) SS BOND : bond 0.00336 ( 39) SS BOND : angle 2.02784 ( 78) covalent geometry : bond 0.00417 (19345) covalent geometry : angle 0.71811 (26253) *********************** 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 366 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 293 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8468 (mt) cc_final: 0.8110 (pp) REVERT: A 426 MET cc_start: 0.6895 (tmm) cc_final: 0.5811 (tmm) REVERT: A 474 ASP cc_start: 0.5564 (OUTLIER) cc_final: 0.5352 (p0) REVERT: B 599 TRP cc_start: 0.8778 (m100) cc_final: 0.8407 (m100) REVERT: C 10 GLN cc_start: 0.7412 (mp10) cc_final: 0.6919 (mp10) REVERT: C 48 MET cc_start: 0.7599 (mtp) cc_final: 0.7361 (mtp) REVERT: C 65 GLN cc_start: 0.8419 (tp40) cc_final: 0.8109 (tp40) REVERT: C 90 ASP cc_start: 0.5612 (t70) cc_final: 0.5305 (t0) REVERT: C 94 TYR cc_start: 0.7378 (m-10) cc_final: 0.7119 (m-10) REVERT: D 625 TYR cc_start: 0.7893 (m-80) cc_final: 0.7666 (m-80) REVERT: E 377 ASN cc_start: 0.7811 (p0) cc_final: 0.7535 (p0) REVERT: E 494 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8746 (tt) REVERT: F 634 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7349 (mt-10) REVERT: H 3 GLN cc_start: 0.7118 (tp-100) cc_final: 0.6652 (mp10) REVERT: H 10 GLN cc_start: 0.7062 (mp-120) cc_final: 0.6663 (mp-120) REVERT: H 65 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7805 (tp40) REVERT: H 81 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7697 (ttp) REVERT: I 298 LYS cc_start: 0.8900 (tttt) cc_final: 0.8327 (tttp) REVERT: K 67 ASN cc_start: 0.8096 (t0) cc_final: 0.7670 (t0) REVERT: K 122 LEU cc_start: 0.8389 (mt) cc_final: 0.7991 (pp) REVERT: K 213 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7431 (tm-30) REVERT: K 379 ASN cc_start: 0.7607 (p0) cc_final: 0.7256 (p0) REVERT: M 90 ASP cc_start: 0.5129 (t70) cc_final: 0.4886 (t70) REVERT: N 262 HIS cc_start: 0.7169 (OUTLIER) cc_final: 0.6138 (t-90) REVERT: N 263 ASP cc_start: 0.7932 (t0) cc_final: 0.7522 (t0) REVERT: N 270 GLN cc_start: 0.5928 (pt0) cc_final: 0.5692 (pt0) REVERT: N 278 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7094 (t80) outliers start: 73 outliers final: 53 residues processed: 340 average time/residue: 0.2907 time to fit residues: 155.2162 Evaluate side-chains 341 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 283 time to evaluate : 2.042 ------------------------------------------------------------------------------- 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 120 VAL 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 444 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain D residue 538 THR 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 42 VAL Chi-restraints excluded: chain E residue 89 VAL 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 374 HIS Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 595 ILE 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 I residue 249 THR Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 120 VAL 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 426 ILE Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain L residue 540 THR Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 571 THR 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 234 LEU Chi-restraints excluded: chain N residue 249 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 4 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 219 optimal weight: 20.0000 chunk 210 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119456 restraints weight = 33287.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121408 restraints weight = 23078.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123327 restraints weight = 18079.184| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19420 Z= 0.160 Angle : 0.755 38.803 26439 Z= 0.348 Chirality : 0.046 0.207 3028 Planarity : 0.004 0.054 3289 Dihedral : 8.297 89.306 3257 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.41 % Favored : 93.46 % Rotamer: Outliers : 3.37 % Allowed : 17.68 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2310 helix: 0.12 (0.27), residues: 396 sheet: -0.68 (0.20), residues: 638 loop : -1.46 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 35 HIS 0.008 0.001 HIS A 374 PHE 0.020 0.002 PHE K 85 TYR 0.021 0.001 TYR I 278 ARG 0.006 0.000 ARG N 311 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 12) link_NAG-ASN : angle 2.47015 ( 36) link_ALPHA1-6 : bond 0.00674 ( 3) link_ALPHA1-6 : angle 1.27757 ( 9) link_BETA1-4 : bond 0.00620 ( 12) link_BETA1-4 : angle 1.96723 ( 36) link_ALPHA1-2 : bond 0.00316 ( 6) link_ALPHA1-2 : angle 1.69726 ( 18) link_ALPHA1-3 : bond 0.01049 ( 3) link_ALPHA1-3 : angle 1.43042 ( 9) hydrogen bonds : bond 0.03587 ( 582) hydrogen bonds : angle 5.23374 ( 1635) SS BOND : bond 0.00281 ( 39) SS BOND : angle 1.97437 ( 78) covalent geometry : bond 0.00372 (19345) covalent geometry : angle 0.73829 (26253) *********************** 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 361 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 292 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8519 (mt) cc_final: 0.8231 (pp) REVERT: A 474 ASP cc_start: 0.5651 (OUTLIER) cc_final: 0.5396 (p0) REVERT: B 599 TRP cc_start: 0.8780 (m100) cc_final: 0.8396 (m100) REVERT: C 48 MET cc_start: 0.7630 (mtp) cc_final: 0.7387 (mtp) REVERT: C 65 GLN cc_start: 0.8361 (tp40) cc_final: 0.8111 (tp40) REVERT: D 584 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7667 (t80) REVERT: E 377 ASN cc_start: 0.7808 (p0) cc_final: 0.7530 (p0) REVERT: E 494 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8749 (tt) REVERT: F 634 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7375 (mt-10) REVERT: H 3 GLN cc_start: 0.6971 (tp-100) cc_final: 0.6695 (mp10) REVERT: H 10 GLN cc_start: 0.7041 (mp-120) cc_final: 0.6667 (mp-120) REVERT: H 48 MET cc_start: 0.7135 (mtp) cc_final: 0.6909 (ttm) REVERT: H 65 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7709 (tp40) REVERT: H 72 ARG cc_start: 0.6998 (pmt-80) cc_final: 0.6688 (ppt170) REVERT: H 81 MET cc_start: 0.8363 (tpp) cc_final: 0.7987 (tpp) REVERT: I 270 GLN cc_start: 0.6381 (pt0) cc_final: 0.6146 (pt0) REVERT: K 67 ASN cc_start: 0.8240 (t0) cc_final: 0.7809 (t0) REVERT: K 213 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7202 (tm-30) REVERT: M 46 GLN cc_start: 0.7617 (mt0) cc_final: 0.7407 (mt0) REVERT: N 262 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6118 (t-90) REVERT: N 263 ASP cc_start: 0.7873 (t0) cc_final: 0.7546 (t0) REVERT: N 270 GLN cc_start: 0.5929 (pt0) cc_final: 0.5711 (pt0) REVERT: N 278 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7180 (t80) REVERT: N 280 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.6514 (mt) outliers start: 69 outliers final: 52 residues processed: 335 average time/residue: 0.3376 time to fit residues: 175.0111 Evaluate side-chains 339 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 281 time to evaluate : 1.956 ------------------------------------------------------------------------------- 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 120 VAL 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 341 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 584 TYR 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 89 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 154 MET Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 494 LEU 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 H residue 102 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 120 VAL 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 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 K residue 483 SER Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 249 THR Chi-restraints excluded: chain N residue 262 HIS Chi-restraints excluded: chain N residue 278 TYR Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain N residue 294 PHE 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 126 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 chunk 195 optimal weight: 0.0770 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 overall best weight: 2.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118738 restraints weight = 33609.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121593 restraints weight = 22778.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123531 restraints weight = 17450.945| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3052 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= 0.170 Angle : 0.767 38.691 26439 Z= 0.357 Chirality : 0.047 0.222 3028 Planarity : 0.004 0.054 3289 Dihedral : 8.007 89.487 3257 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.38 % Rotamer: Outliers : 3.52 % Allowed : 18.41 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2310 helix: 0.15 (0.27), residues: 395 sheet: -0.64 (0.21), residues: 602 loop : -1.45 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 427 HIS 0.008 0.001 HIS A 374 PHE 0.019 0.002 PHE A 85 TYR 0.022 0.001 TYR I 278 ARG 0.007 0.000 ARG N 311 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 12) link_NAG-ASN : angle 2.47863 ( 36) link_ALPHA1-6 : bond 0.00791 ( 3) link_ALPHA1-6 : angle 1.15756 ( 9) link_BETA1-4 : bond 0.00669 ( 12) link_BETA1-4 : angle 1.89239 ( 36) link_ALPHA1-2 : bond 0.00342 ( 6) link_ALPHA1-2 : angle 1.69602 ( 18) link_ALPHA1-3 : bond 0.01019 ( 3) link_ALPHA1-3 : angle 1.46916 ( 9) hydrogen bonds : bond 0.03609 ( 582) hydrogen bonds : angle 5.22404 ( 1635) SS BOND : bond 0.00344 ( 39) SS BOND : angle 2.05290 ( 78) covalent geometry : bond 0.00396 (19345) covalent geometry : angle 0.75109 (26253) *********************** 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 361 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 289 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8504 (mt) cc_final: 0.8207 (pp) REVERT: B 599 TRP cc_start: 0.8786 (m100) cc_final: 0.8411 (m100) REVERT: C 48 MET cc_start: 0.7622 (mtp) cc_final: 0.7359 (mtp) REVERT: C 65 GLN cc_start: 0.8345 (tp40) cc_final: 0.8139 (tp40) REVERT: D 584 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7450 (t80) REVERT: E 377 ASN cc_start: 0.7968 (p0) cc_final: 0.7648 (p0) REVERT: E 494 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8719 (tt) REVERT: H 3 GLN cc_start: 0.7019 (tp-100) cc_final: 0.6681 (mp10) REVERT: H 10 GLN cc_start: 0.7000 (mp-120) cc_final: 0.6591 (mp-120) REVERT: H 65 GLN cc_start: 0.8121 (tp-100) cc_final: 0.7749 (tp40) REVERT: H 72 ARG cc_start: 0.7022 (pmt-80) cc_final: 0.6765 (ppt170) REVERT: I 270 GLN cc_start: 0.6453 (pt0) cc_final: 0.6212 (pt0) REVERT: K 67 ASN cc_start: 0.8305 (t0) cc_final: 0.7843 (t0) REVERT: K 379 ASN cc_start: 0.7599 (p0) cc_final: 0.7232 (p0) REVERT: M 46 GLN cc_start: 0.7704 (mt0) cc_final: 0.7462 (mt0) REVERT: N 262 HIS cc_start: 0.7126 (OUTLIER) cc_final: 0.6095 (t-90) REVERT: N 278 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7219 (t80) REVERT: N 280 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.6438 (mt) outliers start: 72 outliers final: 57 residues processed: 335 average time/residue: 0.3042 time to fit residues: 156.8314 Evaluate side-chains 350 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 288 time to evaluate : 1.996 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 245 VAL 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 450 THR Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 584 TYR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 89 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 154 MET Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 569 THR 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 H residue 102 ILE Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 120 VAL 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 418 LEU Chi-restraints excluded: chain K residue 426 ILE Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain K residue 496 LEU Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 249 THR Chi-restraints excluded: chain N residue 262 HIS Chi-restraints excluded: chain N residue 278 TYR Chi-restraints excluded: chain N residue 280 ILE Chi-restraints excluded: chain N residue 335 THR 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 74 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 223 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 330 HIS ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN L 632 GLN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 292 ASN N 301 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.142510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119269 restraints weight = 33072.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.122254 restraints weight = 22029.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124296 restraints weight = 16676.742| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19420 Z= 0.123 Angle : 0.735 36.618 26439 Z= 0.340 Chirality : 0.045 0.199 3028 Planarity : 0.004 0.051 3289 Dihedral : 7.229 89.512 3257 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.89 % Favored : 93.98 % Rotamer: Outliers : 2.10 % Allowed : 19.92 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.18), residues: 2310 helix: 0.44 (0.27), residues: 396 sheet: -0.38 (0.20), residues: 653 loop : -1.41 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 35 HIS 0.005 0.001 HIS A 374 PHE 0.019 0.001 PHE K 85 TYR 0.014 0.001 TYR I 278 ARG 0.008 0.000 ARG N 311 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 12) link_NAG-ASN : angle 2.20330 ( 36) link_ALPHA1-6 : bond 0.00980 ( 3) link_ALPHA1-6 : angle 1.03864 ( 9) link_BETA1-4 : bond 0.00629 ( 12) link_BETA1-4 : angle 1.80280 ( 36) link_ALPHA1-2 : bond 0.00314 ( 6) link_ALPHA1-2 : angle 1.63040 ( 18) link_ALPHA1-3 : bond 0.01067 ( 3) link_ALPHA1-3 : angle 1.35335 ( 9) hydrogen bonds : bond 0.03193 ( 582) hydrogen bonds : angle 5.00614 ( 1635) SS BOND : bond 0.00370 ( 39) SS BOND : angle 1.84546 ( 78) covalent geometry : bond 0.00275 (19345) covalent geometry : angle 0.72125 (26253) ********************** 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 343 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 300 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 THR cc_start: 0.6433 (m) cc_final: 0.6153 (p) REVERT: B 599 TRP cc_start: 0.8711 (m100) cc_final: 0.8303 (m100) REVERT: C 36 TRP cc_start: 0.8054 (m100) cc_final: 0.7761 (m100) REVERT: D 584 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.7345 (t80) REVERT: D 585 MET cc_start: 0.5496 (ptp) cc_final: 0.4860 (mtm) REVERT: E 377 ASN cc_start: 0.7804 (p0) cc_final: 0.7507 (p0) REVERT: H 3 GLN cc_start: 0.7121 (tp-100) cc_final: 0.6876 (mp10) REVERT: H 10 GLN cc_start: 0.6933 (mp-120) cc_final: 0.6559 (mp-120) REVERT: H 65 GLN cc_start: 0.8058 (tp-100) cc_final: 0.7696 (tp40) REVERT: I 270 GLN cc_start: 0.6354 (pt0) cc_final: 0.6109 (pt0) REVERT: K 115 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8540 (p) REVERT: M 36 TRP cc_start: 0.8502 (m100) cc_final: 0.8147 (m100) REVERT: M 46 GLN cc_start: 0.7692 (mt0) cc_final: 0.7412 (mt0) REVERT: N 262 HIS cc_start: 0.7092 (OUTLIER) cc_final: 0.6786 (t-90) REVERT: N 278 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7148 (t80) REVERT: N 280 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.6546 (mt) REVERT: N 319 TYR cc_start: 0.8211 (m-80) cc_final: 0.8007 (m-80) outliers start: 43 outliers final: 34 residues processed: 326 average time/residue: 0.3322 time to fit residues: 168.9408 Evaluate side-chains 315 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 2.073 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 584 TYR 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 154 MET Chi-restraints excluded: chain F residue 569 THR 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 H residue 102 ILE Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 115 SER 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 483 SER Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 262 HIS Chi-restraints excluded: chain N residue 278 TYR Chi-restraints excluded: chain N residue 280 ILE 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 61 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 217 optimal weight: 0.0970 chunk 51 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 203 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 545 ASN ** 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** N 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113767 restraints weight = 33488.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.116808 restraints weight = 21365.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118886 restraints weight = 15781.750| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3280 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= 0.124 Angle : 0.729 34.586 26439 Z= 0.343 Chirality : 0.045 0.196 3028 Planarity : 0.004 0.051 3289 Dihedral : 6.876 89.813 3257 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.45 % Favored : 93.42 % Rotamer: Outliers : 2.05 % Allowed : 20.31 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.18), residues: 2310 helix: 0.49 (0.27), residues: 396 sheet: -0.30 (0.20), residues: 647 loop : -1.38 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP K 35 HIS 0.006 0.001 HIS A 374 PHE 0.019 0.001 PHE E 85 TYR 0.014 0.001 TYR I 278 ARG 0.008 0.000 ARG N 311 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 12) link_NAG-ASN : angle 2.16831 ( 36) link_ALPHA1-6 : bond 0.01072 ( 3) link_ALPHA1-6 : angle 0.95340 ( 9) link_BETA1-4 : bond 0.00592 ( 12) link_BETA1-4 : angle 1.67537 ( 36) link_ALPHA1-2 : bond 0.00339 ( 6) link_ALPHA1-2 : angle 1.60457 ( 18) link_ALPHA1-3 : bond 0.01001 ( 3) link_ALPHA1-3 : angle 1.33072 ( 9) hydrogen bonds : bond 0.03267 ( 582) hydrogen bonds : angle 4.94199 ( 1635) SS BOND : bond 0.00212 ( 39) SS BOND : angle 1.79124 ( 78) covalent geometry : bond 0.00278 (19345) covalent geometry : angle 0.71594 (26253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5918.21 seconds wall clock time: 107 minutes 16.77 seconds (6436.77 seconds total)