Starting phenix.real_space_refine on Mon May 19 15:27:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8saq_40275/05_2025/8saq_40275_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8saq_40275/05_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_40275/05_2025/8saq_40275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8saq_40275/05_2025/8saq_40275.map" model { file = "/net/cci-nas-00/data/ceres_data/8saq_40275/05_2025/8saq_40275_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8saq_40275/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.74, per 1000 atoms: 0.57 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: 5.07 Conformation dependent library (CDL) restraints added in 2.3 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: 2.44 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: 6.86 Time building geometry restraints manager: 5.75 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 42.660 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.120 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.290 ------------------------------------------------------------------------------- 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 : 2.074 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: 0.3072 time to fit residues: 181.0923 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 : 1.985 ------------------------------------------------------------------------------- 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 = 33083.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126644 restraints weight = 22911.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128340 restraints weight = 17094.399| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 1.46763 ( 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 : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.7952 (m-40) cc_final: 0.7674 (m-40) REVERT: A 426 MET cc_start: 0.6937 (tmm) cc_final: 0.6002 (tmm) REVERT: B 506 MET cc_start: 0.7626 (mtp) cc_final: 0.7366 (mtp) REVERT: B 519 ASN cc_start: 0.9090 (t0) cc_final: 0.8823 (t0) REVERT: D 625 TYR cc_start: 0.7655 (m-80) cc_final: 0.7302 (m-80) REVERT: E 113 ASP cc_start: 0.8169 (t0) cc_final: 0.7921 (t0) REVERT: E 115 SER cc_start: 0.8812 (t) cc_final: 0.8562 (p) REVERT: E 377 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.7109 (p0) REVERT: F 626 MET cc_start: 0.6919 (ttm) cc_final: 0.6425 (ttm) REVERT: F 634 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7298 (mt-10) REVERT: H 3 GLN cc_start: 0.7188 (tp-100) cc_final: 0.6953 (mp10) REVERT: H 4 LEU cc_start: 0.6411 (mm) cc_final: 0.6168 (mm) REVERT: H 10 GLN cc_start: 0.7043 (mp-120) cc_final: 0.6678 (mp-120) REVERT: I 298 LYS cc_start: 0.8958 (tttt) cc_final: 0.8303 (tttp) REVERT: M 48 MET cc_start: 0.7500 (mtp) cc_final: 0.7085 (mtp) REVERT: N 270 GLN cc_start: 0.5660 (pt0) cc_final: 0.5351 (pt0) outliers start: 27 outliers final: 15 residues processed: 319 average time/residue: 0.2996 time to fit residues: 147.2848 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 : 4.091 ------------------------------------------------------------------------------- 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: 9.9990 chunk 139 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 66 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 135 optimal weight: 0.3980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN M 6 GLN ** N 236 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 = 0.3839 r_free = 0.3839 target = 0.142889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119382 restraints weight = 32896.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122309 restraints weight = 22250.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124301 restraints weight = 16987.690| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19420 Z= 0.146 Angle : 0.723 34.115 26439 Z= 0.343 Chirality : 0.046 0.230 3028 Planarity : 0.004 0.053 3289 Dihedral : 9.791 89.395 3257 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.10 % Favored : 93.72 % Rotamer: Outliers : 1.42 % Allowed : 10.16 % Favored : 88.43 % 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: -1.26 (0.18), residues: 2310 helix: 0.23 (0.27), residues: 391 sheet: -0.83 (0.20), residues: 693 loop : -1.15 (0.19), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 35 HIS 0.005 0.001 HIS A 374 PHE 0.018 0.002 PHE E 85 TYR 0.020 0.002 TYR I 278 ARG 0.004 0.000 ARG I 293 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 12) link_NAG-ASN : angle 2.35120 ( 36) link_ALPHA1-6 : bond 0.00383 ( 3) link_ALPHA1-6 : angle 1.45476 ( 9) link_BETA1-4 : bond 0.00630 ( 12) link_BETA1-4 : angle 2.33683 ( 36) link_ALPHA1-2 : bond 0.00284 ( 6) link_ALPHA1-2 : angle 1.96637 ( 18) link_ALPHA1-3 : bond 0.01262 ( 3) link_ALPHA1-3 : angle 1.27606 ( 9) hydrogen bonds : bond 0.03923 ( 582) hydrogen bonds : angle 5.50667 ( 1635) SS BOND : bond 0.00687 ( 39) SS BOND : angle 2.24816 ( 78) covalent geometry : bond 0.00332 (19345) covalent geometry : angle 0.70155 (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 327 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 298 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8272 (mt) cc_final: 0.7989 (pp) REVERT: A 426 MET cc_start: 0.6808 (tmm) cc_final: 0.5811 (tmm) REVERT: B 519 ASN cc_start: 0.9172 (t0) cc_final: 0.8898 (t0) REVERT: C 10 GLN cc_start: 0.7377 (mp10) cc_final: 0.7067 (mp10) REVERT: C 70 MET cc_start: 0.8103 (mtm) cc_final: 0.7827 (mtm) REVERT: E 113 ASP cc_start: 0.8204 (t0) cc_final: 0.7941 (t0) REVERT: E 115 SER cc_start: 0.8845 (t) cc_final: 0.8588 (p) REVERT: E 377 ASN cc_start: 0.7289 (p0) cc_final: 0.7080 (p0) REVERT: F 626 MET cc_start: 0.6829 (ttm) cc_final: 0.6446 (ttm) REVERT: H 3 GLN cc_start: 0.7122 (tp-100) cc_final: 0.6889 (mp10) REVERT: H 10 GLN cc_start: 0.7062 (mp-120) cc_final: 0.6669 (mp-120) REVERT: M 48 MET cc_start: 0.7535 (mtp) cc_final: 0.7190 (mtp) REVERT: N 263 ASP cc_start: 0.7684 (t0) cc_final: 0.7289 (t0) REVERT: N 270 GLN cc_start: 0.5635 (pt0) cc_final: 0.5261 (pt0) outliers start: 29 outliers final: 19 residues processed: 315 average time/residue: 0.2994 time to fit residues: 144.7711 Evaluate side-chains 282 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 263 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain 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 345 VAL Chi-restraints excluded: chain I residue 338 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 86 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 58 optimal weight: 0.4980 chunk 156 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- 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** D 607 ASN E 66 HIS H 54 GLN ** I 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 480 ASN M 3 GLN ** N 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.116059 restraints weight = 33442.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.118887 restraints weight = 22748.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120832 restraints weight = 17458.534| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19420 Z= 0.202 Angle : 0.753 37.833 26439 Z= 0.356 Chirality : 0.047 0.190 3028 Planarity : 0.004 0.051 3289 Dihedral : 9.410 89.441 3257 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.27 % Favored : 92.55 % Rotamer: Outliers : 2.25 % Allowed : 12.40 % Favored : 85.35 % 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: -1.33 (0.18), residues: 2310 helix: 0.25 (0.27), residues: 391 sheet: -0.80 (0.21), residues: 618 loop : -1.27 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 35 HIS 0.011 0.002 HIS E 374 PHE 0.018 0.002 PHE A 85 TYR 0.025 0.002 TYR I 278 ARG 0.005 0.001 ARG D 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 12) link_NAG-ASN : angle 2.57056 ( 36) link_ALPHA1-6 : bond 0.00428 ( 3) link_ALPHA1-6 : angle 1.40465 ( 9) link_BETA1-4 : bond 0.00686 ( 12) link_BETA1-4 : angle 2.27977 ( 36) link_ALPHA1-2 : bond 0.00301 ( 6) link_ALPHA1-2 : angle 1.94025 ( 18) link_ALPHA1-3 : bond 0.01052 ( 3) link_ALPHA1-3 : angle 1.41201 ( 9) hydrogen bonds : bond 0.04014 ( 582) hydrogen bonds : angle 5.46522 ( 1635) SS BOND : bond 0.00228 ( 39) SS BOND : angle 1.99280 ( 78) covalent geometry : bond 0.00473 (19345) covalent geometry : angle 0.73435 (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 334 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8321 (mt) cc_final: 0.8072 (pp) REVERT: A 426 MET cc_start: 0.6965 (tmm) cc_final: 0.5852 (tmm) REVERT: A 467 THR cc_start: 0.6605 (m) cc_final: 0.6309 (p) REVERT: A 474 ASP cc_start: 0.5723 (OUTLIER) cc_final: 0.5195 (p0) REVERT: B 506 MET cc_start: 0.7783 (mtp) cc_final: 0.7491 (mtp) REVERT: B 519 ASN cc_start: 0.9194 (t0) cc_final: 0.8850 (t0) REVERT: B 599 TRP cc_start: 0.8751 (m100) cc_final: 0.8300 (m100) REVERT: C 3 GLN cc_start: 0.6533 (mp-120) cc_final: 0.6279 (mp10) REVERT: C 10 GLN cc_start: 0.7407 (mp10) cc_final: 0.6980 (mp-120) REVERT: E 113 ASP cc_start: 0.8302 (t0) cc_final: 0.8035 (t0) REVERT: E 115 SER cc_start: 0.8882 (t) cc_final: 0.8621 (p) REVERT: E 377 ASN cc_start: 0.7548 (p0) cc_final: 0.7283 (p0) REVERT: F 530 MET cc_start: 0.7732 (mtp) cc_final: 0.7442 (mtp) REVERT: F 634 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7102 (mt-10) REVERT: H 3 GLN cc_start: 0.7219 (tp-100) cc_final: 0.6855 (mp10) REVERT: H 10 GLN cc_start: 0.7017 (mp-120) cc_final: 0.6634 (mp-120) REVERT: H 72 ARG cc_start: 0.6789 (pmt-80) cc_final: 0.6558 (ppt170) REVERT: H 105 TYR cc_start: 0.8257 (m-80) cc_final: 0.7908 (m-80) REVERT: K 122 LEU cc_start: 0.8363 (mt) cc_final: 0.8030 (pp) REVERT: K 379 ASN cc_start: 0.7471 (p0) cc_final: 0.7149 (p0) REVERT: N 263 ASP cc_start: 0.7605 (t0) cc_final: 0.7197 (t0) REVERT: N 270 GLN cc_start: 0.5953 (pt0) cc_final: 0.5579 (pt0) outliers start: 46 outliers final: 34 residues processed: 317 average time/residue: 0.2933 time to fit residues: 142.7168 Evaluate side-chains 313 residues out of total 2048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 278 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain K residue 207 CYS Chi-restraints excluded: chain K residue 241 CYS Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 347 VAL Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain L residue 568 VAL Chi-restraints excluded: chain L residue 583 LEU Chi-restraints excluded: chain L residue 644 ILE Chi-restraints excluded: chain N residue 294 PHE Chi-restraints excluded: chain N residue 338 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.5619 > 50: distance: 84 - 86: 5.236 distance: 86 - 87: 6.774 distance: 87 - 88: 10.387 distance: 88 - 89: 8.526 distance: 90 - 91: 4.110 distance: 91 - 92: 9.809 distance: 91 - 94: 14.711 distance: 92 - 93: 15.994 distance: 92 - 104: 5.067 distance: 94 - 95: 3.508 distance: 95 - 96: 4.821 distance: 95 - 97: 7.194 distance: 96 - 98: 6.909 distance: 97 - 99: 13.918 distance: 97 - 100: 10.770 distance: 98 - 99: 15.879 distance: 99 - 101: 13.271 distance: 100 - 102: 3.924 distance: 101 - 103: 5.204 distance: 104 - 105: 17.491 distance: 105 - 106: 15.472 distance: 105 - 108: 14.478 distance: 106 - 107: 29.336 distance: 106 - 112: 15.215 distance: 108 - 109: 10.900 distance: 108 - 110: 29.365 distance: 109 - 111: 5.898 distance: 112 - 113: 19.006 distance: 113 - 114: 20.359 distance: 113 - 116: 19.115 distance: 114 - 115: 30.295 distance: 114 - 118: 17.709 distance: 116 - 117: 20.995 distance: 118 - 119: 19.421 distance: 119 - 120: 21.278 distance: 119 - 122: 23.860 distance: 120 - 121: 9.268 distance: 120 - 126: 19.977 distance: 122 - 123: 26.333 distance: 123 - 124: 17.174 distance: 123 - 125: 13.085 distance: 126 - 127: 9.592 distance: 127 - 128: 6.833 distance: 127 - 130: 17.720 distance: 128 - 129: 19.822 distance: 128 - 138: 5.879 distance: 130 - 131: 3.976 distance: 131 - 132: 8.386 distance: 131 - 133: 8.130 distance: 132 - 134: 9.017 distance: 133 - 135: 12.939 distance: 134 - 136: 9.042 distance: 135 - 136: 6.745 distance: 136 - 137: 11.038 distance: 138 - 139: 13.257 distance: 139 - 140: 10.880 distance: 139 - 142: 8.458 distance: 140 - 141: 10.820 distance: 140 - 150: 12.220 distance: 142 - 143: 6.743 distance: 143 - 144: 4.319 distance: 143 - 145: 7.111 distance: 144 - 146: 3.316 distance: 145 - 147: 5.429 distance: 146 - 148: 3.332 distance: 148 - 149: 5.055 distance: 150 - 151: 9.154 distance: 151 - 152: 7.873 distance: 151 - 154: 4.480 distance: 152 - 153: 20.378 distance: 152 - 158: 8.292 distance: 154 - 155: 6.249 distance: 155 - 156: 7.943 distance: 155 - 157: 9.157 distance: 158 - 159: 8.398 distance: 159 - 160: 6.377 distance: 159 - 162: 12.049 distance: 160 - 161: 21.186 distance: 160 - 164: 15.098 distance: 162 - 163: 33.759 distance: 164 - 165: 6.975 distance: 165 - 166: 7.504 distance: 165 - 168: 6.520 distance: 166 - 167: 4.602 distance: 166 - 170: 21.051 distance: 168 - 169: 9.234